- absolute() - Method in class Tuple3d
-
Convert each dimension's component into its absolute value.
- AbsoluteValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- AbsoluteValue() - Constructor for class AbsoluteValue
-
- accept(S, T) - Method in interface CheckedBiConsumer
-
Calls the function.
- accept(S) - Method in interface CheckedConsumer
-
Like Consumer.accept(T) but throws an exception.
- accept(int) - Method in interface CheckedIntConsumer
-
Like IntConsumer.accept(int) but throws an exception.
- accept(BinaryVoxels<UnsignedByteBuffer>) - Method in class AcceptIterationList
-
- accept(BinaryVoxels<UnsignedByteBuffer>) - Method in interface AcceptIterationPredicate
-
Whether a particular voxels fulfills the condition or not.
- accept(int, int) - Method in interface Histogram.BinConsumer
-
Accepts a particular bin and corresponding count.
- accept(ObjectMask, ObjectMask, ObjectMask) - Method in interface AfterCondition
-
- accept(ObjectMask) - Method in class AndCondition
-
- accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in interface BeforeCondition
-
- accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in class DistanceCondition
-
- accept(ObjectMask, ObjectMask, ObjectMask) - Method in class IncreaseFeatureCondition
-
- accept(ObjectMask) - Method in class NeighborhoodCondition
-
- accept(ObjectMask) - Method in interface UpdatableBeforeCondition
-
- accept(ObjectMask) - Method in class WrapAsUpdatable
-
- accept(ParsedFilePathBag) - Method in class AtLeastZSlices
-
- accept(ParsedFilePathBag) - Method in class CheckParsedFilePathBag
-
- accept(Point2i, int) - Method in interface OffsettedPointTwoDimensionalConsumer
-
Accepts a point like with a
Consumer in general.
- accept(int, int, int) - Method in interface OffsettedScalarTwoDimensionalConsumer
-
Accepts a point
- accept(Point2i) - Method in interface PointTwoDimensionalConsumer
-
Accepts a point like with a
Consumer in general.
- accept(int, int, int) - Method in interface ScalarThreeDimensionalConsumer
-
Accepts a point like with a
Consumer in general.
- accept(int, int) - Method in interface ScalarTwoDimensionalConsumer
-
Accepts a point like with a
Consumer in general.
- acceptableProbability(AnnealScheme) - Method in class AssignMode
-
- acceptableProbability(AnnealScheme) - Method in class DirectAssignMode
-
- acceptableProbability(AnnealScheme) - Method in class TransformationAssignMode
-
- AcceptanceProbabilityCalculator<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization
-
- AcceptanceProbabilityCalculator(AnnealScheme, ExtractScoreSize<T>) - Constructor for class AcceptanceProbabilityCalculator
-
- accepted() - Method in interface DualMarks
-
The accepted marks.
- AcceptIterationList - Class in org.anchoranalysis.image.voxel.object.morphological.predicate
-
- AcceptIterationList() - Constructor for class AcceptIterationList
-
- AcceptIterationPredicate - Interface in org.anchoranalysis.image.voxel.object.morphological.predicate
-
A condition that must be fulfilled for a particular iteration of a morphological operation to be
accepted.
- acceptPathViaRegEx(Path, Pattern) - Static method in class MatchRegularExpression
-
- acceptProposal(ToDoubleFunction<T>) - Method in class OptimizationStep
-
- accepts(Class<?>) - Method in class AssignerMatchClass
-
- accepts(Class<?>) - Method in interface InitializationParameterAssigner
-
Whether a particular type of initialization parameters is accepted?
- AccessObjectMask<T> - Interface in org.anchoranalysis.image.core.object.scale
-
Provides functions to provide access and creation to/from the object-mask representation of a
generic type.
- AccessObjectMaskSimple - Class in org.anchoranalysis.image.core.object.scale
-
Provides access to the simple-case of a list of
ObjectMasks.
- AccessObjectMaskSimple() - Constructor for class AccessObjectMaskSimple
-
- AcquisitionDateReader - Class in org.anchoranalysis.io.bioformats.metadata
-
Reads the image acquisition-date.
- activateDebugMode(String) - Method in class ExecutionArguments
-
Activates debug-mode.
- add(NamedBean<?>) - Method in class Define
-
Adds a named-bean to our definitions, using the {#link GroupingRoot} annotation to determine
a group where definitions are stored.
- add(Double) - Method in class DoubleList
-
- add(Double) - Method in class DoubleSet
-
- add(Integer) - Method in class IntegerList
-
- add(Integer) - Method in class IntegerSet
-
- add(T) - Method in interface PrimitiveBeanCollection
-
Add an element to the collection.
- add(String) - Method in class StringList
-
- add(String) - Method in class StringSet
-
- add(Color) - Method in class ColorList
-
Appends a
Color to the list.
- add(RGBColor) - Method in class ColorList
-
- add(int, RGBColor) - Method in class ColorList
-
Inserts a
Color into the list, at a particular index.
- add(String, T) - Method in class NameValueMap
-
Adds an element.
- add(NameValue<T>) - Method in class NameValueMap
-
Adds an element.
- add(String, StoreSupplier<T>) - Method in class EagerEvaluationStore
-
- add(String, StoreSupplier<T>) - Method in class LazyEvaluationStore
-
- add(String, StoreSupplier<T>) - Method in interface NamedProviderStore
-
Adds an element to the store.
- add(StatefulMessageLogger) - Method in class MessageLoggerList
-
- add(Class<? extends InputFromManager>) - Method in class InputTypesExpected
-
- add(SubmittedJob) - Method in class ConcurrentJobMonitor
-
- add(Feature<? extends T>) - Method in class FeatureList
-
Adds a feature to the current list.
- add(LabelledResultsVector) - Method in interface FeatureCalculationResults
-
Adds a results-element to be written.
- add(String) - Method in class FeatureNameList
-
Adds a feature-name.
- add(String, int) - Method in class FeatureNameMapToIndex
-
Adds a new featureName and index
- add(ResultsVector) - Method in class ResultsVectorList
-
- add(CacheTransferSource<? extends FeatureInput>) - Method in class CacheTransferSourceCollection
-
- add(String, Feature<T>) - Method in class NamedFeatureStore
-
Adds a named-feature to the store.
- add(BoundingBox) - Method in class BoundingBoxesOnPlane
-
- add(ObjectMask) - Method in class ObjectCollectionWithProperties
-
Add an
ObjectMask to the collection, assigning empty properties to it.
- add(ObjectWithProperties) - Method in class ObjectCollectionWithProperties
-
- add(String, Stack) - Method in class NamedStacks
-
Add a stack.
- add(String, StoreSupplier<Stack>) - Method in class NamedStacks
-
- add(String, Stack) - Method in class NamedStacksUniformSize
-
Adds an element to the store.
- add(RasterGenerator<T>) - Method in class CombineRasterGenerator
-
- add(ChannelEntry) - Method in class NamedEntries
-
- add(NamedChannelsForSeries) - Method in class NamedChannelsForSeriesConcatenate
-
- add(Stack) - Method in class StackSeries
-
- add(Stack) - Method in class TimeSequence
-
- add(String, StoreSupplier<TimeSequence>) - Method in class WrapStackAsTimeSequenceStore
-
- add(AcceptIterationPredicate) - Method in class AcceptIterationList
-
Adds an item to the list of predicates.
- add(ObjectMask) - Method in class ObjectCollection
-
Adds an object to the collection.
- add(VoxelStatistics) - Method in class VoxelStatisticsCombined
-
Adds an element.
- add(String, Generator<T>) - Method in class CombinedListGenerator
-
- add(FileType[]) - Method in class ConcatenateFileTypes
-
- add(T) - Method in class OutputSequenceIncrementing
-
Outputs an additional element in the sequence.
- add(T, S) - Method in class OutputSequenceIndexed
-
Outputs an additional element in the sequence.
- add(T, Optional<S>) - Method in class OutputSequenceIndexed
-
Outputs an additional element in the sequence.
- add(OutputtedFile) - Method in class RootDirectory
-
- add(MutableDirectory) - Method in class RootDirectory
-
- add(OutputtedFile) - Method in class Subdirectory
-
- add(String, boolean) - Method in class RecordedOutputs
-
Adds a new output-name to the set of recorded names.
- add(RunningSum) - Method in class RunningSum
-
Adds the values of another
RunningSum to the current values.
- add(double) - Method in class RunningSumExtrema
-
Adds a value to the running-sum, also remembering if value is the minimum or maximum
of calls to this method.
- add(double) - Method in class VarianceCalculatorDouble
-
Adds a value to the running sum.
- add(int) - Method in class VarianceCalculatorLong
-
Adds a value to the running sum.
- add(int, int) - Method in class VarianceCalculatorLong
-
Adds a multiple instances of a value to the running sum.
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class RandomCollectionWithAddCriteria
-
- add(double) - Method in class EnergyTotal
-
- add(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown
-
- add(VoxelizedMarkMemo) - Method in class MarksWithTotalEnergy
-
- add(VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy
-
- add(EnergyTotal) - Method in class EnergySavedInd
-
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class EnergySavedPairs
-
- add(String, EnergyScheme) - Method in class EnergySchemeSet
-
- add(EnergySavedInd, VoxelizedMarkMemo, EnergyStackWithoutParameters, EnergySchemeWithSharedFeatures) - Method in class EnergyMemoList
-
- add(VoxelizedMarkMemo) - Method in class MemoList
-
- add(UpdatableMarks) - Method in class UpdatableMarksList
-
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class UpdatableMarksList
-
- add(MemoForIndex) - Method in class UpdatableMarksList
-
- add(int, UpdatableMarks) - Method in class UpdatableMarksList
-
- add(IndexByRegion<T>) - Method in class IndexByChannel
-
- add(String, StoreSupplier<T>) - Method in interface MultiInputSubMap
-
Adds an entry to the map
- add(String, StoreSupplier<T>) - Method in class OperationMap
-
- add(String, StoreSupplier<TimeSequence>) - Method in class StackWithMap
-
- add(Mark, Color) - Method in class ColoredMarks
-
- add(Mark, RGBColor) - Method in class ColoredMarks
-
- add(Mark) - Method in class MarkCollection
-
- add(MemoForIndex, VoxelizedMarkMemo) - Method in interface UpdatableMarks
-
- add(String) - Method in class ErrorNode
-
- add(Exception) - Method in class ErrorNode
-
- add(String) - Method in class ErrorNodeImpl
-
- add(Exception) - Method in class ErrorNodeImpl
-
- add(String) - Method in class ErrorNodeNull
-
- add(Exception) - Method in class ErrorNodeNull
-
- add(FeedbackReceiver<T>) - Method in class FeedbackReceiverList
-
- add(TerminationCondition) - Method in class TerminationConditionListOr
-
- add(AggregateReceiver<T>) - Method in class AggregateReceiverList
-
- add(PeriodReceiver<T>) - Method in class PeriodReceiverList
-
- add(WeightedKernel<T, S>) - Method in class WeightedKernelList
-
- add(Overlay, RGBColor) - Method in class ColoredOverlayCollection
-
- add(Overlay) - Method in class OverlayCollection
-
- add(String, String) - Method in class OverlayProperties
-
- add(String, int) - Method in class OverlayProperties
-
- add(double) - Method in class AxisLimits
-
- add(ImageCounter<T>) - Method in class ImageCounterList
-
- add(LevelResult) - Method in class LevelResultCollection
-
- add(CheckedSupplier<LabelledResultsVector, OperationFailedException>, CheckedSupplier<Optional<DisplayStack>, OperationFailedException>) - Method in class FeatureResultsAndThumbnails
-
Adds results, together with a thumbnail.
- add(S, T) - Method in interface AddToAggregateItem
-
- add(Optional<String>, String, S) - Method in class GroupMapByName
-
Adds an item with an identifier
- add(T, String) - Method in class FileLabelMap
-
- add(ImageMetadataInput) - Method in class ImageSize
-
- add(ImageMetadataInput) - Method in class SummarizerImageMetadataSimple
-
- add(T) - Method in class SummarizerInputFromManager
-
- add(Path) - Method in class ExtensionCount
-
- add(Path) - Method in class FilePathPattern
-
- add(Path) - Method in class FileSizeStatistics
-
- add(T) - Method in class Summarizer
-
Adds a element to the summary.
- add(T) - Method in class SummarizerAggregate
-
- add(T) - Method in class SummarizerCount
-
- add(T) - Method in class SummarizerListMultiline
-
- add(T) - Method in class SummarizerSplitMoreThan
-
- add(FileDetails) - Method in class ParsedFilePathBag
-
- add(int, String) - Method in class SortedSetChannel
-
- add(Point3i) - Method in class PointRange
-
Adds a new point to be considered in the range.
- add(int, int, int) - Method in class PointRange
-
Adds a new point to be considered in the range.
- add(Point2i) - Method in class Point2d
-
Arithmetically adds a
Point2i's values across each dimension.
- add(Point2d) - Method in class Point2d
-
Arithmetically adds a
Point2d's values across each dimension.
- add(Point2i) - Method in class Point2i
-
Adds values from a
Point2i across each corresponding dimension.
- add(double, double, double) - Method in class Tuple3d
-
Arithmetically adds values to each dimension's component.
- add(Tuple3d) - Method in class Tuple3d
-
Arithmetically adds a
Tuple3d's values across each dimension.
- add(ReadableTuple3i) - Method in class Tuple3d
-
- add(ReadableTuple3i) - Method in class Tuple3i
-
- add(BoundingBox, T) - Method in class BoundingBoxRTree
-
Adds a bounding-box with a corresponding payload.
- add(double, double, T) - Method in class IntervalRTree
-
Adds a bounding-box with a corresponding index.
- add(Rectangle, T) - Method in class RTree
-
Adds a Rectangle with a corresponding payload.
- addAdditionalOptions(Options) - Method in class LauncherConfig
-
- addAdditionalOptions(Options) - Static method in class CommandLineOptions
-
- addAll(Define) - Method in class Define
-
Adds all the named-beans from source to the current map.
- addAll(List<NamedBean<T>>) - Method in class Define
-
Adds all the named-beans from source to the current map.
- addAll(ColorList) - Method in class ColorList
-
Appends
Colors to the list.
- addAll(FeatureList<? extends T>) - Method in class FeatureList
-
Add all the features in other to the current list.
- addAll(ObjectCollection) - Method in class ObjectCollection
-
Adds all objects in objects to the collection.
- addAll(Collection<? extends ObjectMask>) - Method in class ObjectCollection
-
Adds all objects in collection to the collection.
- addAll(MemoForIndex) - Method in class MemoList
-
- addAll(Collection<? extends UpdatableMarks>) - Method in class UpdatableMarksList
-
- addAll(int, Collection<? extends UpdatableMarks>) - Method in class UpdatableMarksList
-
- addAll(MarkCollection, RGBColor) - Method in class ColoredMarks
-
- addAll(ColoredMarks) - Method in class ColoredMarks
-
- addAll(MarkCollection) - Method in class MarkCollection
-
- addAll(OverlayCollection) - Method in class OverlayCollection
-
- addAll(Collection<S>) - Method in class ImageCounterList
-
- addAll(Collection<T>) - Method in class Summarizer
-
Adds the elements to the summary.
- addAllOutputNamesTo(OutputEnabledMutable) - Method in class DefineOutputter
-
- addAllToUpdatablePairList(UpdatableMarksList) - Method in class VoxelizedMarksWithEnergy
-
- addAnnotatedImage(T) - Method in interface ImageCounter
-
Add an image that had an associated annotation.
- addAnnotatedImage(T) - Method in class ImageCounterList
-
- addAsSeparateChannels(NamedStacks, int, Progress, Logger) - Method in interface NamedChannelsForSeries
-
- addAsSeparateChannels(NamedProviderStore<TimeSequence>, int, Logger) - Method in interface NamedChannelsForSeries
-
- addAsSeparateChannels(NamedStacks, int, Progress, Logger) - Method in class NamedChannelsForSeriesConcatenate
-
- addAsSeparateChannels(NamedProviderStore<TimeSequence>, int, Logger) - Method in class NamedChannelsForSeriesConcatenate
-
- addAsSeparateChannels(NamedStacks, int, Progress, Logger) - Method in class NamedChannelsForSeriesMap
-
- addAsSeparateChannels(NamedProviderStore<TimeSequence>, int, Logger) - Method in class NamedChannelsForSeriesMap
-
- addAssignedPair(ObjectMask, ObjectMask, double) - Method in class OverlappingObjects
-
Adds an assigned pair of objects with a particular overlap-ratio.
- addBasicOptions(Options) - Static method in class CommandLineOptions
-
- addBlankChannel() - Method in class Stack
-
Adds a new empty
Channel in the final-most position in the list.
- addChangeID(Mark, Color) - Method in class ColoredMarks
-
- addChangeID(Mark, RGBColor) - Method in class ColoredMarks
-
- addChannel(Channel) - Method in class Stack
-
Appends a channel to the stack, as the new final-most channel position-wise.
- addChannel(Channel) - Method in class StackNotUniformSized
-
Appends a channel to the stack, as the new final-most channel positionwise.
- addChannelsFrom(Stack) - Method in class Stack
-
Add the channels from another instance into this instance.
- AddConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- AddConstant() - Constructor for class AddConstant
-
- AddConstantTo<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- AddConstantTo() - Constructor for class AddConstantTo
-
- AddCriteria<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria
-
Add Criteria
- AddCriteriaEnergyPair - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaEnergyPair(FeatureList<FeatureInputPairMemo>, AddCriteriaPair) - Constructor for class AddCriteriaEnergyPair
-
- AddCriteriaFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
-
- AddCriteriaFeatureRelationThreshold() - Constructor for class AddCriteriaFeatureRelationThreshold
-
- AddCriteriaNever<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaNever() - Constructor for class AddCriteriaNever
-
- AddCriteriaOr - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaOr() - Constructor for class AddCriteriaOr
-
- AddCriteriaPair - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- AddCriteriaPair() - Constructor for class AddCriteriaPair
-
- addDefaultOutputs(OutputEnabledMutable) - Method in class AnnotationComparisonAssigner
-
Adds any default outputs that should occur from the assigner.
- addDefaultOutputs(OutputEnabledMutable) - Method in class FeatureCostAssigner
-
- addDefaultOutputs(OutputEnabledMutable) - Method in class MaskIntersectionAssigner
-
- addDictionary(String, Dictionary) - Method in class ImageInitialization
-
Adds a dictionary to named-collection of dictionaries.
- AddDistanceTransform - Class in org.anchoranalysis.plugin.fiji.bean.define
-
- AddDistanceTransform() - Constructor for class AddDistanceTransform
-
- addDouble(String, double) - Method in class StatisticsToExport
-
Adds a statistic that is a double.
- addDoubleAsString(String, double) - Method in class OverlayProperties
-
- AddDualTransformer - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
-
- AddDualTransformer() - Constructor for class AddDualTransformer
-
- addEdge(V, V) - Method in class GraphWithoutPayload
-
Add an edge between two vertices.
- addEdge(V, V, P) - Method in class GraphWithPayload
-
Add an edge between two vertices.
- AddEdgeFilters - Class in org.anchoranalysis.plugin.imagej.bean.define
-
- AddEdgeFilters() - Constructor for class AddEdgeFilters
-
- addEdges(V, Collection<V>) - Method in class GraphWithoutPayload
-
Adds edge(s) from the vertex from to each element in toCollection.
- addEnabledOutputFirst(String...) - Method in class OutputEnabledMutable
-
Adds enabled first-level outputs.
- addEnabledOutputs(OutputEnabledMutable) - Method in class OutputEnabledMutable
-
- addEnabledOutputSecond(String, String...) - Method in class OutputEnabledMutable
-
Adds enabled second-level outputs.
- AddEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
-
- AddEnergy() - Constructor for class AddEnergy
-
- addErrorDescription(StringBuilder) - Method in class ErrorNode
-
- addErrorDescription(StringBuilder) - Method in class ErrorNodeImpl
-
- addErrorDescription(StringBuilder) - Method in class ErrorNodeNull
-
- addErrorLevel(String) - Method in class ProposerContext
-
- addFormatted(String, Object...) - Method in class ErrorNode
-
- addFormatted(String, Object...) - Method in class ErrorNodeImpl
-
- addFormatted(String, Object...) - Method in class ErrorNodeNull
-
- addForSlice(int, int) - Method in interface VoxelPartition
-
- addForSlice(int, int) - Method in class VoxelPartitionHistogram
-
- addFrom(BeanInstanceMap) - Method in class BeanInstanceMap
-
Populates the entries from another BeanInstanceMap
- addFrom(List<NamedBean<?>>) - Method in class BeanInstanceMap
-
- addFrom(NamedProvider<Stack>) - Method in class NamedStacks
-
- addFrom(CommandLineExtracter, InputArguments) - Static method in class AddInputOptions
-
Adds options to change the inputs from the command-line.
- addFrom(CommandLineExtracter, OutputArguments) - Static method in class AddOutputOptions
-
Adds options to add/remove change the outputs the inputs from the command-line.
- addFromList(FeatureList<FeatureInput>) - Method in class SharedFeatures
-
Add features from a feature-list.
- addFromProviders(NamedProvider<FeatureList<FeatureInput>>) - Method in class SharedFeatures
-
- addFromWithPrefix(NamedProvider<Stack>, String) - Method in class NamedStacks
-
- addFromXmlFile(Path) - Method in class RootPathMap
-
Adds root-paths contained in a list of XML Beans in an xml file
- addHistogram(Histogram) - Method in class Histogram
-
Adds the counts from another histogram to the current object.
- addIgnoreInfinity(double) - Method in class AxisLimits
-
- addInputOptions(Options) - Static method in class CommandLineOptions
-
- AddInputOptions - Class in org.anchoranalysis.launcher.options.process
-
Adds options relating to inputting from the command-line.
- addInt(String, int) - Method in class StatisticsToExport
-
Adds a statistic that is an int.
- additionalLabelsFor(FileInput) - Method in class FromHistogram
-
- additionalLabelsFor(ProvidesStackInput) - Method in class FromImage
-
- additionalLabelsFor(ImageMetadataInput) - Method in class FromImageMetadata
-
- additionalLabelsFor(T) - Method in class SingleRowPerInput
-
Additional labels for an input to include (after the identifier, and before any group
labels).
- addLabelToDataset(DefaultCategoryDataset, T, int, String, String) - Method in class BarPlot
-
- addLabelToDataset(DefaultBoxAndWhiskerCategoryDataset, T, int, String, String) - Method in class BoxPlot
-
- addLabelToDataset(S, T, int, String, String) - Method in class PlotIndexBaseCategorical
-
- addManifestExperimentFileSet(Collection<File>, ManifestDeserializer, Logger) - Method in class ManifestCouplingDefinition
-
- addMeanExtrema(String, double, double, double) - Method in class StatisticsToExport
-
Adds three statistics a mean, min and max.
- addMeanExtrema(String, RunningSumExtrema) - Method in class StatisticsToExport
-
- addMultiple(RGBColor, int) - Method in class ColorList
-
Append multiple entries for the same color to the end of the list.
- addObjectsNoBoundingBoxChange(Collection<T>) - Method in class BoundedList
-
Adds elements without changing the bounding-box
- addObjectsToGraph(ObjectCollection) - Method in class MergeGraph
-
- addObjectsWithColor(ObjectCollectionProvider, RGBColor) - Method in class ColoredObjectCollection
-
- addOperationRecorder(WriteOperationRecorder) - Method in class Outputter
-
- addOperationRecorder(WriteOperationRecorder) - Method in class OutputterChecked
-
Adds an additional operation recorder alongside any existing recorders.
- addOptionsFromCommandLine() - Method in class AddInputOptions
-
- AddOptionsFromCommandLine<T> - Class in org.anchoranalysis.launcher.options.process
-
Base class for adding options from command-line arguments.
- AddOptionsFromCommandLine(CommandLineExtracter, T) - Constructor for class AddOptionsFromCommandLine
-
- addOptionsFromCommandLine() - Method in class AddOptionsFromCommandLine
-
Maybe add options to the arguments from the command-line.
- addOptionsFromCommandLine() - Method in class AddOutputOptions
-
- AddOutputOptions - Class in org.anchoranalysis.launcher.options.process
-
Adds options relating to outputting from the command-line.
- addResultsFor(LabelledResultsVector) - Method in class GroupedResults
-
Adds a result to the group-writer, but doesn't write yet.
- addRow(LabelledResultsVector) - Method in class FeatureCSVWriter
-
Directly adds a row of feature-values.
- addRow(List<TypedValue>) - Method in class FeatureCSVWriter
-
Directly adds a row in the form of typed-values.
- addSharedObjectsDictionary(Optional<SharedObjects>, Optional<Dictionary>) - Method in class ImageInitialization
-
- addShift(ReadableTuple3i) - Method in class ContiguousVoxelPath
-
Adds a shift to each point (modifying the existing points in memory), and returns them as a
list
- addSlice(VoxelBuffer<T>) - Method in interface ProjectableBuffer
-
Adds a slice to the buffer.
- addStack(Provider<Stack>) - Method in class ArrangeRaster
-
Adds a stack to the existing list of stack-providers.
- addString(String, String) - Method in class StatisticsToExport
-
Adds a statistic that is a
String.
- addTimestamp(long) - Method in class ClusterIdentifier
-
Adds a timestamp to the cluster.
- addTo(Define) - Method in class Concatenate
-
- addTo(Define) - Method in interface DefineAdder
-
Adds items to define.
- addTo(Define) - Method in class FromXMLList
-
- addTo(ObjectMask, int) - Method in interface VoxelsArithmetic
-
Adds a constant-value to each voxel but only for voxels inside an object-mask.
- addTo(Define) - Method in class AddDistanceTransform
-
- addTo(S, T) - Method in class GroupMapByName
-
- addTo(Define) - Method in class AddEdgeFilters
-
- addTo(Define) - Method in class VisualizeOnBackground
-
- AddToAggregateItem<S,T> - Interface in org.anchoranalysis.plugin.image.task.grouped
-
Adds an individual-item to an aggregate-item
- AddToDefaults - Class in org.anchoranalysis.io.output.bean.rules
-
Adds additional outputs-names to be enabled to the defaults.
- AddToDefaults() - Constructor for class AddToDefaults
-
- addToErrorNode(ErrorNode) - Method in exception ErrorNodeException
-
- addToManager(MultiInputManager, String, String) - Method in class FilePathBaseAppendToManager
-
- addToRow(List<TypedValue>) - Method in class RowLabels
-
Adds the identifiers to a row to be outputted in a features CSV.
- addToStacks(String, Stack) - Method in class ImageInitialization
-
- addToStacks(String, StackProvider) - Method in class ImageInitialization
-
- addToStore(NamedProviderStore<T>, Logger) - Method in interface MultiInputSubMap
-
- addToStore(NamedProviderStore<T>, Logger) - Method in class OperationMap
-
- addToStore(NamedProviderStore<TimeSequence>, Logger) - Method in class StackWithMap
-
- addToStore(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class StackWithMap
-
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class NamedChannelsInput
-
- addToStoreInferNames(NamedProviderStore<Stack>, Logger) - Method in interface ProvidesStackInput
-
Adds the current object to a named-store of stacks (using the default series).
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in interface ProvidesStackInput
-
Adds the current object to a named-store of stacks.
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class MultiInput
-
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class ConvertNamedChannelsInputToStack
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class NamedChannelsInput
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in interface ProvidesStackInput
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class MultiInput
-
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, Progress, Logger) - Method in class ConvertNamedChannelsInputToStack
-
- addToUpdatablePairList(UpdatableMarksList, VoxelizedMarkMemo) - Method in class VoxelizedMarksWithEnergy
-
- addToVoxelList(int, int, int) - Method in class IndexByRegion
-
- addTypedValuesTo(Collection<TypedValue>, int) - Method in class ResultsVector
-
- addUnannotatedImage() - Method in interface ImageCounter
-
Add an image that did not have an associated annotation.
- addUnannotatedImage() - Method in class ImageCounterList
-
- addUnassignedLeft(ObjectMask) - Method in class OverlappingObjects
-
Add an unassigned object to the left set.
- addUnassignedLeft(ObjectCollection) - Method in class OverlappingObjects
-
Add unassigned objects to the left set.
- addUnassignedRight(ObjectMask) - Method in class OverlappingObjects
-
Add an unassigned object to the right set.
- addUnassignedRight(ObjectCollection) - Method in class OverlappingObjects
-
Add unassigned objects to the right set.
- addUncoupledJobs(Collection<File>, ManifestDeserializer, Logger) - Method in class ManifestCouplingDefinition
-
Adds job-manifests that don't have corresponding experiment-manifests.
- addUnused(T) - Method in interface VoxelPartitionFactory
-
- addUnused(Histogram) - Method in class VoxelPartitonFactoryHistogram
-
- addVertex(V) - Method in class GraphWithoutPayload
-
Adds a vertex.
- addVertex(V) - Method in class GraphWithPayload
-
Adds a vertex.
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOption
-
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionDual
-
- addWeightedKernelFactories(List<WeightedKernel<T, S>>) - Method in class KernelProposerOptionSingle
-
- addWithName(Define, String, AnchorBean<?>) - Method in class DefineAdderWithPrefixBean
-
Add an item to define with a name being added.
- addWithUnits(String, double, DoubleUnaryOperator, SpatialUnits.UnitSuffix) - Method in class OverlayProperties
-
- AdjacentFile - Class in org.anchoranalysis.plugin.quick.bean.input
-
- AdjacentFile() - Constructor for class AdjacentFile
-
- adjacentVerticesOutgoing(V) - Method in class GraphWithoutPayload
-
The vertices that are connected to a particular vertex by an outgoing edge.
- adjacentVerticesOutgoing(V) - Method in class GraphWithPayload
-
The vertices that are connected to a particular vertex by an outgoing edge.
- adjacentVerticesOutgoingStream(V) - Method in class GraphWithoutPayload
-
- adjacentVerticesOutgoingStream(V) - Method in class GraphWithPayload
-
- afterAllJobsAreExecuted(S, InputOutputContext) - Method in class Task
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class TaskWithoutSharedState
-
- afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class AggregateAnnotations
-
- afterAllJobsAreExecuted(ComparisonSharedState<T>, InputOutputContext) - Method in class CompareAnnotations
-
- afterAllJobsAreExecuted(FeatureExporter<S>, InputOutputContext) - Method in class ExportFeatures
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ConvertImageFormat
-
- afterAllJobsAreExecuted(GroupedSharedState<S, T>, InputOutputContext) - Method in class GroupedStackBase
-
- afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T>, InputOutputContext) - Method in class ImageAssignLabel
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ScaleImage
-
- afterAllJobsAreExecuted(SharedStateSegmentInstance<T>, InputOutputContext) - Method in class SegmentInstanceWithModel
-
- afterAllJobsAreExecuted(SharedStateSelectedSlice, InputOutputContext) - Method in class ExtractSlice
-
- afterAllJobsAreExecuted(OutputSequenceIncrementing<Stack>, InputOutputContext) - Method in class MovieFromSlices
-
- afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class CombineCSV
-
- afterAllJobsAreExecuted(RecordingCounter<T>, InputOutputContext) - Method in class CopyFiles
-
- afterAllJobsAreExecuted(Summarizer<S>, InputOutputContext) - Method in class SummarizeBase
-
- afterAllJobsAreExecuted(SharedStateRememberConverted<U, S>, InputOutputContext) - Method in class ConvertNamedChannels
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ExportReportFeaturesFromManifest
-
- afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class ExportReportFeaturesFromMulti
-
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class ExportObjectsAsCroppedImages
-
- afterAllJobsAreExecuted(FromCSVSharedState, InputOutputContext) - Method in class ExportObjectsFromCSV
-
- afterAllJobsAreExecuted(ExperimentState, InputOutputContext) - Method in class SegmentMarksFromImage
-
- AfterCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitScheduler
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerAnd
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerConvexAboutRoot
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerMaxDistanceAlongContour
-
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class VisitSchedulerUniformSample
-
- aggEnd(Aggregator) - Method in interface AggregateReceiver
-
- aggEnd(Aggregator) - Method in class AggregateReceiverList
-
- aggEnd(Aggregator) - Method in class ConsoleAggregatedReporter
-
- aggEnd(Aggregator) - Method in class CSVReporterAggregated
-
- aggEnd(Aggregator) - Method in class Log4JReporter
-
- aggEnd(Aggregator) - Method in class OptimizationStepLogReporter
-
- aggEnd(Aggregator) - Method in class TextFile
-
- AggIDCounter - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggIDCounter(int) - Constructor for class AggIDCounter
-
- AggregateAnnotations<S extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
-
Aggregates many per-image annotations together in form of a CSV file.
- AggregateAnnotations() - Constructor for class AggregateAnnotations
-
- AggregateReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregateReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregateReceiverList() - Constructor for class AggregateReceiverList
-
- aggregateResults(List<Double>) - Method in class FeatureIntersectingObjectsSingleElement
-
- aggregateResults(List<Double>) - Method in class MaxFeatureIntersectingObjects
-
- aggregateResults(List<Double>) - Method in class MinFeatureIntersectingObjectsAboveThreshold
-
- aggregateResults(List<Double>) - Method in class NumberIntersectingObjectsAboveThreshold
-
- AggregateTriggerBank<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregateTriggerBank(ExtractScoreSize<T>) - Constructor for class AggregateTriggerBank
-
- Aggregator - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- Aggregator(int) - Constructor for class Aggregator
-
- AggregatorException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
- AggregatorException() - Constructor for exception AggregatorException
-
- AggregatorException(String) - Constructor for exception AggregatorException
-
- AggregatorException(Exception) - Constructor for exception AggregatorException
-
- aggReport(Reporting<T>, Aggregator) - Method in interface AggregateReceiver
-
- aggReport(Reporting<T>, Aggregator) - Method in class AggregateReceiverList
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class ConsoleAggregatedReporter
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class CSVReporterAggregated
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class Log4JReporter
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class OptimizationStepLogReporter
-
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class TextFile
-
- aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in interface AggregateReceiver
-
- aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in class AggregateReceiverList
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class ConsoleAggregatedReporter
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class CSVReporterAggregated
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class Log4JReporter
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class OptimizationStepLogReporter
-
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class TextFile
-
- All - Class in org.anchoranalysis.io.output.bean.enabled
-
All outputs are allowed irrespective of outputName.
- All - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects all possible channels from all possible stacks
- All() - Constructor for class All
-
- allAssociatedPaths() - Method in interface InputFromManager
-
- allChannelsAsStack(int, Logger) - Method in interface NamedChannelsForSeries
-
- allChannelsAsStack(int, Logger) - Method in class NamedChannelsForSeriesConcatenate
-
- allChannelsAsStack(int, Logger) - Method in class NamedChannelsForSeriesMap
-
- allChannelsEightBit() - Method in class StackWriteAttributes
-
Mark the attributes to indicate that channels are no longer guaranteed to be 8-bit.
- allChannelsHaveIdenticalType() - Method in class Stack
-
Determines if all channels have an identical voxel data-type.
- allChannelsHaveType(VoxelDataType) - Method in class RGBStack
-
Determines if all channels have a specific data-type.
- allChannelsHaveType(VoxelDataType) - Method in class Stack
-
Determines if all channels have a specific data-type.
- allChannelsHaveType(VoxelDataType) - Method in class TimeSequence
-
- allExtensions() - Method in enum ImageFileFormat
-
All extensions associated with a file-format.
- allFileTypes() - Method in class ConcatenateFileTypes
-
- allHeaders() - Method in class LabelHeaders
-
The non-group and group headers combined (in this order respectively)
- allImageExtensions() - Static method in class FormatExtensions
-
- allLabels(NoSharedState) - Method in class BinaryOutcomeImageLabeller
-
- allLabels(ImageCSVLabellerInitialization) - Method in class ImageCSVLabeller
-
- allLabels(T) - Method in class ImageLabeller
-
A set of identifiers for all groups that can be outputted by the labeller.
- allLabels(ImageLabellerStringMapInitialization<T>) - Method in class ImageLabellerStringMap
-
- allMatchIntensity(ObjectMask, Voxels<T>, IntPredicate) - Static method in class IterateVoxelsObjectMask
-
Do all points on an object-mask match a predicate on the point's voxel-intensity?
- allocate(int) - Static method in class UnsignedByteBuffer
-
Allocates a new buffer of unsigned-bytes.
- allocate(int) - Static method in class UnsignedIntBuffer
-
Allocates a new (direct) buffer of unsigned-ints.
- allocate(int) - Static method in class UnsignedShortBuffer
-
Allocates a new (direct) buffer of unsigned-shorts.
- allocateFloat(int) - Static method in class VoxelBufferFactory
-
Allocates a new float voxel-buffers of given size.
- allocateFloatArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of float voxel-buffers of given size.
- allocateUnsignedByte(int) - Static method in class VoxelBufferFactory
-
Allocates a new unsigned byte voxel-buffer of given size.
- allocateUnsignedByteArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of unsigned byte voxel-buffers of given size.
- allocateUnsignedInt(int) - Static method in class VoxelBufferFactory
-
Allocates a new unsigned int voxel-buffers of given size.
- allocateUnsignedIntArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of unsigned int voxel-buffers of given size.
- allocateUnsignedShort(int) - Static method in class VoxelBufferFactory
-
Allocates a new unsigned short voxel-buffers of given size.
- allocateUnsignedShortArray(int) - Static method in class VoxelBufferFactory
-
Creates an array of unsigned short voxel-buffers of given size.
- AllowEmpty - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a String is allowed be empty, otherwise by default it must be non-empty.
- AllSlicesMaskEverythingNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Only considers voxels with non-zero intensity.
- AllSlicesMaskEverythingNonZero() - Constructor for class AllSlicesMaskEverythingNonZero
-
- AllSlicesMaskNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Gets all slices where indexNonZero has at least one non-zero pixel in that slice
- AllSlicesMaskNonZero() - Constructor for class AllSlicesMaskNonZero
-
- allSuccessful() - Method in class TaskStatistics
-
Did all jobs execute and completely successfully?
- AllValuesOff - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
Creates a new mask of particular dimensionality where all values are off.
- AllValuesOff() - Constructor for class AllValuesOff
-
- AllValuesOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
Creates a new mask of particular dimensionality where all values are on.
- AllValuesOn() - Constructor for class AllValuesOn
-
- ALPHA - Static variable in class RGBChannelNames
-
Name for the alpha channel.
- Always - Class in org.anchoranalysis.plugin.image.bean.object.match
-
Specifies a single object that will always be the "match" for whatever source object.
- Always() - Constructor for class Always
-
- always2D(String) - Static method in class OutputSequenceStackFactory
-
The stacks that are outputted are guaranteed to be two-dimensional.
- always2D(boolean) - Method in class StackWriteAttributes
-
- AlwaysAllowed - Class in org.anchoranalysis.io.output.writer
-
Allows every output, irrespective of whether the
OutputterChecked allows the output-name.
- AlwaysAllowed(ElementOutputter, Optional<WriterExecuteBeforeEveryOperation>) - Constructor for class AlwaysAllowed
-
- alwaysExecuteBeforeCallingLibrary() - Static method in class CVInit
-
This routine must always be executed at least once before calling any routines in the OpenCV
library
- AlwaysNew<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.replace
-
Always create a new session-input with no reuse or caching.
- AlwaysNew(CacheCreator) - Constructor for class AlwaysNew
-
Constructor with default means of creating a session-input
- AlwaysNew(CacheCreator, ChildCacheFinder) - Constructor for class AlwaysNew
-
- AlwaysReject - Class in org.anchoranalysis.plugin.io.bean.metadata.reader
-
- AlwaysReject() - Constructor for class AlwaysReject
-
- AnchorBean<F> - Class in org.anchoranalysis.bean
-
The base class of all beans used in
Anchor.
- AnchorBean() - Constructor for class AnchorBean
-
- AnchorBeanFactory - Class in org.anchoranalysis.bean.xml.factory
-
Base class for all Anchor-specific bean factories.
- AnchorBeanFactory() - Constructor for class AnchorBeanFactory
-
- AnchorCheckedException - Exception in org.anchoranalysis.core.exception
-
A base class for all checked exceptions used on the Anchor platform.
- AnchorCheckedException() - Constructor for exception AnchorCheckedException
-
Creates without message or cause.
- AnchorCheckedException(String, Throwable) - Constructor for exception AnchorCheckedException
-
Creates with message and cause.
- AnchorCheckedException(String) - Constructor for exception AnchorCheckedException
-
Creates with only a message.
- AnchorCheckedException(Throwable) - Constructor for exception AnchorCheckedException
-
Creates with only a cause.
- AnchorCombinableException - Exception in org.anchoranalysis.core.exception.combinable
-
An exception that can be combined with similar exceptions and summarized.
- AnchorCombinableException(String, Throwable) - Constructor for exception AnchorCombinableException
-
Creates with a description and a cause.
- AnchorDefaultBeanFactory - Class in org.anchoranalysis.bean.xml.factory
-
The default bean factory used for initializing
AnchorBeans.
- AnchorDefaultBeanFactory(BeanInstanceMap) - Constructor for class AnchorDefaultBeanFactory
-
- AnchorFriendlyCheckedException - Exception in org.anchoranalysis.core.exception.friendly
-
A base class for particular checked-exceptions which are guaranteed to provide a user-friendly
error description.
- AnchorFriendlyCheckedException(String, Throwable) - Constructor for exception AnchorFriendlyCheckedException
-
A user-friendly error message and its cause.
- AnchorFriendlyCheckedException(String) - Constructor for exception AnchorFriendlyCheckedException
-
A user-friendly error message WITHOUT a cause.
- AnchorFriendlyCheckedException(Throwable) - Constructor for exception AnchorFriendlyCheckedException
-
A wrapped exception.
- AnchorFriendlyRuntimeException - Exception in org.anchoranalysis.core.exception.friendly
-
A base class for particular runtime-exceptions which are guaranteed to provide a user-friendly
error description.
- AnchorFriendlyRuntimeException(String, Throwable) - Constructor for exception AnchorFriendlyRuntimeException
-
A user-friendly error message and its cause.
- AnchorFriendlyRuntimeException(String) - Constructor for exception AnchorFriendlyRuntimeException
-
A user-friendly error message without a cause.
- AnchorFriendlyRuntimeException(Throwable) - Constructor for exception AnchorFriendlyRuntimeException
-
A wrapped exception.
- AnchorImpossibleSituationException - Exception in org.anchoranalysis.core.exception.friendly
-
A run-time exception to throw in situations which should never logically occur by design.
- AnchorImpossibleSituationException() - Constructor for exception AnchorImpossibleSituationException
-
Default constructor.
- AnchorImpossibleSituationException(String) - Constructor for exception AnchorImpossibleSituationException
-
Creates with a specific message explaining the exception.
- AnchorNeverOccursException - Exception in org.anchoranalysis.core.exception
-
This is an exceotion that should never be thrown, but can be used for type-safety where an
exception is needed
- AnchorNeverOccursException() - Constructor for exception AnchorNeverOccursException
-
- AnchorRuntimeException - Exception in org.anchoranalysis.core.exception
-
A base class for all unchecked (runtime) exceptions used on the Anchor platform.
- AnchorRuntimeException() - Constructor for exception AnchorRuntimeException
-
Creates without message or cause.
- AnchorRuntimeException(String, Throwable) - Constructor for exception AnchorRuntimeException
-
Creates with message and cause.
- AnchorRuntimeException(String) - Constructor for exception AnchorRuntimeException
-
Creates with only a message.
- AnchorRuntimeException(Throwable) - Constructor for exception AnchorRuntimeException
-
Creates with only a cause.
- AnchorWebsiteLinks - Class in org.anchoranalysis.launcher
-
A centralized location for hyperlinks to the Anchor website.
- and(StackWriteAttributes) - Method in class StackWriteAttributes
-
- And - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation and voxelwise on both masks, modifying {mask} with the
result.
- And() - Constructor for class And
-
- And - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
Applies multiples filter with logical AND i.e.
- And() - Constructor for class And
-
- AndCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
-
Combines two UpdatableBeforeConditions as LOGICAL ANDs
- AndCondition(UpdatableBeforeCondition, UpdatableBeforeCondition) - Constructor for class AndCondition
-
- AndKernel - Class in org.anchoranalysis.image.voxel.kernel
-
Combines two
BinaryKernels so that they only a true value exists only at a point where
both kernels return true.
- AndKernel(BinaryKernel, BinaryKernel) - Constructor for class AndKernel
-
Create for the two kernels.
- AndList - Class in org.anchoranalysis.plugin.mpp.bean.check
-
- AndList() - Constructor for class AndList
-
- AndObjectsWithMasks - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask
-
Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
- AndObjectsWithMasks() - Constructor for class AndObjectsWithMasks
-
- AnisotropicDiffusion - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider
-
- AnisotropicDiffusion() - Constructor for class AnisotropicDiffusion
-
- AnnealScheme - Class in org.anchoranalysis.mpp.bean
-
- AnnealScheme() - Constructor for class AnnealScheme
-
- Annotation - Interface in org.anchoranalysis.annotation
-
Base class for types of image annotations.
- AnnotationAggregateCSVGenerator - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
-
- AnnotationAggregateCSVGenerator() - Constructor for class AnnotationAggregateCSVGenerator
-
- AnnotationBackground - Class in org.anchoranalysis.annotation.io.bean
-
How to display one or more
Stacks as background during an annotation process.
- AnnotationBackground() - Constructor for class AnnotationBackground
-
- AnnotationComparisonAssigner<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
-
Compares elements in an annotation to elements from an experiment.
- AnnotationComparisonAssigner() - Constructor for class AnnotationComparisonAssigner
-
- AnnotationComparisonInput<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.comparison
-
- AnnotationComparisonInput(T, Tuple2<ComparableSource, ComparableSource>, Tuple2<String, String>, StackReader) - Constructor for class AnnotationComparisonInput
-
- AnnotationComparisonInputManager<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
-
- AnnotationComparisonInputManager() - Constructor for class AnnotationComparisonInputManager
-
- AnnotationDeleter - Interface in org.anchoranalysis.annotation.io
-
Allows an annotation to be deleted from the file-system.
- annotationExistsAt(Path) - Method in class DualMarksAnnotationReader
-
Whether an annotation exists at a particular path on the file-system.
- AnnotationInputManager<T extends ProvidesStackInput,S extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io.bean
-
An
InputManager that provides annotations corresponding to images.
- AnnotationInputManager() - Constructor for class AnnotationInputManager
-
- AnnotationLabel - Class in org.anchoranalysis.plugin.annotation.bean.label
-
- AnnotationLabel() - Constructor for class AnnotationLabel
-
- annotationLabelFor(ProvidesStackInput, Logger) - Method in class AnnotatorStrategy
-
A human-friendly textual description of the annotation, or
Optional.empty() if no
label is available.
- annotationLabelFor(ProvidesStackInput, Logger) - Method in class ImageLabelStrategy
-
- annotationLabelFor(ProvidesStackInput, Logger) - Method in class MarkProposerStrategy
-
- AnnotationReader<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
-
Allows an annotation to be read from the file-system.
- AnnotationWithMarks - Interface in org.anchoranalysis.annotation.mark
-
An image-annotation that involves a mark-collection.
- AnnotationWithStrategy<T extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io
-
One particular annotation, associated with its strategy.
- AnnotationWithStrategy(ProvidesStackInput, T) - Constructor for class AnnotationWithStrategy
-
Creates for a particular input and associated annotation strategy.
- AnnotationWriter<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
-
Allows an annotation to be written to the file-system.
- AnnotatorStrategy - Class in org.anchoranalysis.annotation.io.bean
-
How an input is associated with annotations on the file-system, and how this is presented
visually.
- AnnotatorStrategy() - Constructor for class AnnotatorStrategy
-
- Anonymize - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Copies files to a number 001, 002 etc.
- Anonymize() - Constructor for class Anonymize
-
- AnonymizeSharedState - Class in org.anchoranalysis.plugin.io.shared
-
- AnonymizeSharedState(NumberToStringConverter, Map<Integer, Integer>) - Constructor for class AnonymizeSharedState
-
- any() - Method in class VoxelsUntyped
-
Exposes without any specific buffer type.
- anyDimensionIsLargerThan(Extent) - Method in class Extent
-
Returns true if any dimension in this extent is larger than the corresponding dimension in
other extent.
- anyExists() - Method in class PredicateAtCorner
-
- anyExists() - Method in class PredicateImplementation
-
- anyExists() - Method in interface VoxelsPredicate
-
Does at least one value satisfy the predicate - across all voxels?
- anyMatch(Predicate<ObjectMask>) - Method in class ObjectMaskStream
-
Does the predicate evaluate to true on any object in the collection?
- anyPredicateMatch(Voxels<T>, Predicate<T>) - Static method in class IterateVoxelsAll
-
Tries to apply a predicate to all the remaining buffer locations, returning true if the
predicate matches.
- AnySliceCenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
-
The center ps of at least one slice should be on the stack Tries overall center point first, and
then projects it onto each slice
- AnySliceCenterOnMask() - Constructor for class AnySliceCenterOnMask
-
- append(StatisticsToExport) - Method in class StatisticsToExport
-
Appends the names and values from another AnnotationComparison to the existing.
- append(Optional<FeatureList<T>>) - Method in class FeatureList
-
Appends the features one or more (optional) feature-lists to the existing list.
- AppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A CSV that is appended from the root of a project
- AppendCsv() - Constructor for class AppendCsv
-
- AppendDictionary - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendDictionary() - Constructor for class AppendDictionary
-
- appendExtension(String, Optional<String>) - Static method in class ExtensionUtilities
-
Appends an (optional) extension to a string, adding in the leading period if the extension is
defined.
- appendExtension(Path, Optional<String>) - Static method in class ExtensionUtilities
-
- AppendFilePath - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendFilePath() - Constructor for class AppendFilePath
-
- AppendHistogram - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendHistogram() - Constructor for class AppendHistogram
-
- AppendMarks - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendMarks() - Constructor for class AppendMarks
-
- AppendObjects - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
- AppendObjects() - Constructor for class AppendObjects
-
- AppendStack - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A stack from a stack-collection
- AppendStack() - Constructor for class AppendStack
-
- AppendStackDirect - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A stack from a stack-collection
- AppendStackDirect() - Constructor for class AppendStackDirect
-
- apply(Throwable, Writer, String, int, boolean) - Static method in class RecursivelyDescribeExceptionStack
-
Incrementally adds a line to a string builder with the message of each exception moving onto
the next nested exception until there are no more
- apply(S, T) - Method in interface CheckedBiFunction
-
Calls the function.
- apply(S) - Method in interface CheckedFunction
-
Calls the function.
- apply(int) - Method in interface CheckedIntFunction
-
Calls the function
- apply(T) - Method in interface CheckedUnaryOperator
-
Applies the operation.
- apply(int, int) - Method in interface IntBinaryOperation
-
Applies the operation on two integer values.
- apply(ImageInitialization) - Static method in class CreateCombinedStack
-
- apply(Mask, Mask) - Static method in class MaskAnd
-
Performs a logical and operation on each voxel in two masks, writing the result onto
the second mask.
- apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class MaskAnd
-
Performs a logical
and operation on each voxel in two
Voxels (considered to be
masks), writing the result onto the second mask.
- apply(Mask, Mask) - Static method in class MaskOr
-
Performs a logical or operation on each voxel in two masks, writing the result onto
the first mask.
- apply(Mask, Mask) - Static method in class MaskXor
-
Performs a logical xor (exclusive or) operation on each voxel in two masks, writing
the result onto the first mask.
- apply(BinaryVoxels<UnsignedByteBuffer>, BinaryVoxels<UnsignedByteBuffer>) - Static method in class MaskXor
-
Performs a logical
xor (exclusive or) operation on each voxel in two
Voxels
(considered to be masks), writing the result onto the second mask.
- apply(List<ChannelEntry>) - Method in class NamedEntriesCreator
-
- apply(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel
-
Apply the kernel to BinaryVoxels<UnsignedByteBuffer> using the same binary-values as
voxels to calculate a value for each voxel.
- apply(IFormatReader, ReadOptions, int) - Method in class DimensionsCreator
-
- apply(String, Path) - Static method in class WriteStringToFile
-
- applyAsDouble(T, U) - Method in interface CheckedToDoubleBiFunction
-
Applies this function to the given arguments.
- applyAsFloat(int) - Method in interface IntToFloatFunction
-
Applies this function to the given argument.
- applyAsInt(S) - Method in interface CheckedToIntFunction
-
Calls the function
- applyCoefficientsToMark(DoubleMatrix2D, Mark, Dimensions) - Method in class LinearLeastSquaresViaNormalEquationBase
-
- applyDelta(MultiLevelOutputEnabled) - Method in class OutputEnabledDelta
-
Applies the changes to enable or disable additional outputs, if they are defined.
- applyFitResultToMark(Ellipsoid, Dimensions, double) - Method in class FitResult
-
- applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel
-
Applies the kernel to voxels and sums the returned value.
- applyForCount(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class ApplyKernel
-
Applies the kernel to voxels and sums the returned value.
- applyForCount(BinaryKernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters) - Static method in class ApplyKernel
-
Applies a
BinaryKernel to voxels and counts how many true values occur en aggregate.
- ApplyImageJMorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.mask
-
Applies an ImageJ (2D) morphological operation to voxels
- applyInitializationIfPossibleTo(Object, Object, Logger) - Method in class BeanInitializer
-
Applies the initialization to a bean if possible.
- ApplyKernel - Class in org.anchoranalysis.image.voxel.kernel
-
- applyMorphologicalOperation(Mask, boolean) - Method in class Dilate
-
- applyMorphologicalOperation(Mask, boolean) - Method in class Erode
-
- applyMorphologicalOperation(Mask, boolean) - Method in class MorphologicalOperatorBase
-
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class Dilate
-
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class Erode
-
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class ObjectCollectionProviderMorphological
-
- applyOperation(UnaryOperator<Stack>, Optional<Dimensions>) - Method in class NamedStacks
-
Applies an operation on each
Stack in the collection and returns a new derived
collection.
- applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateIncrementalOperationMap
-
- applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateDilationMap
-
- applyOperation(ObjectMask, Extent, boolean) - Method in class CalculateErosionMap
-
- applyOperation(BinaryVoxels<UnsignedByteBuffer>, String, int) - Static method in class ApplyImageJMorphologicalOperation
-
- applyRadiiSubtractScale(double, double) - Method in class FitResult
-
- applyRankFilter(Channel, int, int) - Static method in class FilterHelper
-
Applies a 2D rank-filter to each slice independently.
- applyStrategy(MergeCandidate) - Method in class MergeStrategy
-
- applyUntilPositive(CountKernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters) - Static method in class ApplyKernel
-
Applies the kernel to voxels until a positive value is returned, then exits with true.
- arbitraryElement() - Method in class RTree
-
Any arbitrary element from the tree.
- ArbitraryInsidePoint - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
-
Calculates deterministicly a point that is definitely inside the object-mask.
- ArbitraryInsidePoint(String) - Constructor for class ArbitraryInsidePoint
-
- ArbitraryInsidePoint() - Constructor for class ArbitraryInsidePoint
-
- ArbitraryPointCommon - Class in org.anchoranalysis.mpp.feature.addcriteria
-
If one arbitrarily point overlaps between two MarkPointList then true, otherwise false
- ArbitraryPointCommon() - Constructor for class ArbitraryPointCommon
-
- Area<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
-
Area of the stack (XY dimensions only, Z dimension is not considered).
- Area() - Constructor for class Area
-
- areAllPointsInBigNeighborhood(List<Point3i>) - Static method in class PointsNeighborChecker
-
Are all points in a list neighboring the next point in the list?
- AreaPhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
-
Area expressed in physical coordinates
- AreaPhysical() - Constructor for class AreaPhysical
-
- AreaPixels - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
-
Area expressed as square pixels
- AreaPixels(double) - Constructor for class AreaPixels
-
- AreaPixels() - Constructor for class AreaPixels
-
- areaXY() - Method in class Dimensions
-
Size in X multiplied by size in Y.
- areaXY() - Method in class Extent
-
Size in X multiplied by size in Y.
- areDocumentsEqual(Document, Document) - Static method in class CompareXML
-
Are two XML-documents equal in content, ignoring whitespace and comments?
- areEqual(double, double) - Static method in class DoubleUtilities
-
Are the two numbers equal?
- areEqual(float, float) - Static method in class FloatUtilities
-
Are the two numbers equal?
- arePointsNeighbors(Point3i, Point3i) - Static method in class PointsNeighborChecker
-
Do two points have a big neighbor relationship to each other?
- ArgumentConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path.convert
-
Converts string passed as arguments.
- arithmetic() - Method in class Channel
-
Interface that allows manipulation of voxel intensities via arithmetic operations.
- arithmetic() - Method in class BoundedVoxels
-
Interface that allows manipulation of voxel intensities via arithmetic operations.
- arithmetic() - Method in class Voxels
-
Interface that allows manipulation of voxel intensities via arithmetic operations.
- arithmetic() - Method in class VoxelsUntyped
-
Interface that allows manipulation of voxel intensities via arithmetic operations.
- ArithmeticWithConstantBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a
constant.
- ArithmeticWithConstantBase() - Constructor for class ArithmeticWithConstantBase
-
- ArithmeticWithConstantConditionallyWriteBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- ArithmeticWithConstantConditionallyWriteBase() - Constructor for class ArithmeticWithConstantConditionallyWriteBase
-
- ArrangeRaster - Class in org.anchoranalysis.image.bean.provider.stack
-
Creates a stack that tiles (or otherwise combines) other providers
- ArrangeRaster(boolean, boolean) - Constructor for class ArrangeRaster
-
- ArrangeRaster() - Constructor for class ArrangeRaster
-
- ArrangeStack - Interface in org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
- ArrangeStackBean - Class in org.anchoranalysis.image.bean.spatial.arrange
-
- ArrangeStackBean() - Constructor for class ArrangeStackBean
-
- ArrangeStackException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
- ArrangeStackException(String) - Constructor for exception ArrangeStackException
-
- ArrangeStackException(Exception) - Constructor for exception ArrangeStackException
-
- array() - Method in class UnsignedByteBuffer
-
- array() - Method in class UnsignedIntBuffer
-
- array() - Method in class UnsignedShortBuffer
-
- as(boolean) - Static method in enum OutsideKernelPolicy
-
- asArray(boolean) - Static method in class RGBChannelNames
-
Creates an array with all channel-names in R-G-B order.
- asByte() - Method in class BinaryValuesInt
-
- asByte() - Method in class VoxelsUntyped
-
- asByte(ImageProcessor) - Static method in class ConvertToVoxelBuffer
-
Convert a ImageProcessor to VoxelBuffer<UnsignedByteBuffer>
- asCollection() - Method in class StackSeries
-
- AsCollection - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- AsCollection() - Constructor for class AsCollection
-
- asCollectionOrderNotPreserved() - Method in class ScaledElements
-
Returns the scaled-elements as a collection but without preserving the original element
order.
- asExtent() - Method in class SizeXY
-
Creates an extent with identical width and height and depth (z-extent) of 1
- asExtent(int) - Method in class SizeXY
-
Creates an extent with identical width and height and a specific depth (z-extent)
- asFile() - Method in interface InputFromManager
-
Expresses the input as a file with a name (the unique identifier).
- asFloat() - Method in class VoxelsUntyped
-
- asFloat(ImageProcessor) - Static method in class ConvertToVoxelBuffer
-
Convert a ImageProcessor to VoxelBuffer<FloatBuffer>
- asGraph() - Method in class IntersectingObjects
-
Constructs a graph where each vertex is an element and an edge exists between any elements
that intersect.
- asInt() - Method in class BinaryValuesByte
-
- asInt() - Method in class VoxelsUntyped
-
- asList() - Method in class StringList
-
Exposes the underlying list of values.
- asList() - Method in class FeatureList
-
Exposes the underlying list of features in this data-structure.
- asList() - Method in class FeatureNameList
-
Exposes the underlying list of names.
- asList(boolean) - Static method in class RGBChannelNames
-
Creates a list with all channel-names in R-G-B order.
- asList() - Method in class ObjectCollection
-
Exposes the underlying objects as a list.
- asList() - Method in class OverlayCollection
-
- asListChannels() - Method in class Stack
-
- asListOrderPreserved(List<T>) - Method in class ScaledElements
-
Returns a list of scaled-elements corresponding to a list of unscaled-elements.
- asMap() - Method in class ScaledElements
-
The underlying map used to map an unscaled object to its scaled counterpart.
- AsMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- AsMark() - Constructor for class AsMark
-
- asMarks() - Method in class EnergyMemoList
-
- asNamedStacks() - Method in class NamedStacksUniformSize
-
- AsObject - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- AsObject() - Constructor for class AsObject
-
- asObjectMask() - Method in class ObjectWithProperties
-
Exposes the underlying
ObjectMask ignoring any properties.
- AsObjectMask - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
-
Treats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask
feature
- AsObjectMask() - Constructor for class AsObjectMask
-
- asOperationFailedException() - Method in exception GetOperationFailedException
-
- asPath() - Method in class RootPath
-
Exposes the
path field as a
Path.
- asPath(boolean) - Method in class DirectoryWithPrefix
-
A path that combines the directory and fileNamePrefix and delimiter.
- asPoint() - Method in class Padding
-
- asPredicateDouble() - Method in class RelationToThreshold
-
Expresses the relation as a predicate on values, where only values that fulfill the relation
to threshold are true.
- asPredicateInt() - Method in class RelationToThreshold
-
- asScaleFactor() - Method in class ScaleFactorInt
-
Converts to a
ScaleFactor that accepts floating-point values.
- assertCalc(ResultsVector, Object...) - Static method in class ResultsVectorTestUtilities
-
- assertDoubleResult(String, Feature<T>, T, double) - Static method in class FeatureTestCalculator
-
- assertDoubleResult(String, Feature<T>, T, Optional<SharedObjects>, double) - Static method in class FeatureTestCalculator
-
- assertDoubleResult(String, Feature<T>, T, T, double, double) - Static method in class FeatureTestCalculatorDuo
-
- assertIntResult(String, Feature<T>, T, int) - Static method in class FeatureTestCalculator
-
- assertIntResult(String, Feature<T>, T, Optional<SharedObjects>, int) - Static method in class FeatureTestCalculator
-
- assertIntResult(String, Feature<T>, T, T, int, int) - Static method in class FeatureTestCalculatorDuo
-
- assertValid() - Method in class MarksWithEnergyBreakdown
-
- assertValid() - Method in class EnergySavedInd
-
- assertValid() - Method in class EnergySavedPairs
-
- asSet(boolean) - Static method in class RGBChannelNames
-
Creates a set of the channel names.
- asSet(Progress, Logger) - Method in interface ProvidesStackInput
-
Exposes the input as a set of named stacks (inferring the names).
- asSet() - Method in class RTree
-
All elements contained within the tree, as a
Set.
- asShort() - Method in class VoxelsUntyped
-
- asShort(ImageProcessor) - Static method in class ConvertToVoxelBuffer
-
Convert a ImageProcessor to VoxelBuffer<UnsignedShortBuffer>
- assignAccepted(DualMarks) - Method in class DualMarksAnnotation
-
Assigns marks with an overall accepted state.
- assignBestFromCurrent() - Method in class DualState
-
- assignBoundingBox(BoundingBox) - Method in class BoundedList
-
Assigns a new containing bounding-box.
- assignBoundingBoxAndMap(BoundingBox, UnaryOperator<T>) - Method in class BoundedList
-
Assigns a new containing bounding-box and maps each individual element.
- assignColor(Point3i, RGBColor) - Method in class RGBStack
-
Assigns a
RGBColor to the respective channels for a single voxel.
- assignCopyNonInputs() - Method in class InputArguments
-
- assignCurrent(Optional<T>) - Method in class DualState
-
- assignDescription(ManifestDirectoryDescription) - Method in class MutableDirectory
-
Assigns a description, which may not already exist.
- assignEachMatchingPoint(Voxels<?>, IntPredicate, int) - Static method in class IterateVoxelsAll
-
Assigns a value to any voxel whose intensity matches a predicate, reading and writing the
buffer as an int.
- AssignerMatchClass<P extends BeanInitialization> - Class in org.anchoranalysis.bean.initializable.property
-
Allows assignment of parameters if they are are of type paramTypeMatch or subclass of it.
- AssignerMatchClass(Class<?>) - Constructor for class AssignerMatchClass
-
- AssignFeatureNameUtilities - Class in org.anchoranalysis.feature.name
-
Utilities for assigning a name to a feature.
- assignFilterExtensions(Set<String>) - Method in class InputArguments
-
- assignFilterExtensionsIfMissing(Optional<Set<String>>) - Method in class InputArguments
-
- assignFilterGlob(String) - Method in class InputArguments
-
- assignFrom(Mark) - Method in class VoxelizedMarkMemo
-
Assigns a new mark to replace the existing mark.
- AssignFromChannel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
Copies the pixels from channelAssignFrom to channel (possibly masking)
- AssignFromChannel() - Constructor for class AssignFromChannel
-
- AssignFromDictionary - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
- AssignFromDictionary() - Constructor for class AssignFromDictionary
-
- AssignFromIntersectingObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
Matches source-objects to target objects, based upon intersection, and assigns the value in the
respective source object to the target object
- AssignFromIntersectingObjects() - Constructor for class AssignFromIntersectingObjects
-
- assignFunction(String) - Method in class ManifestDescription
-
Assigns a new function.
- assignIdentifierSubrange(IndexRangeNegative) - Method in class InputArguments
-
If defined, this indicates and specifies only a subset of the elements of the identifier to
use.
- assignInitializationToProperties(Object, Object, Object, Logger) - Method in class AssignerMatchClass
-
- assignInitializationToProperties(Object, Object, Object, Logger) - Method in interface InitializationParameterAssigner
-
Assigns the parameter to the bean.
- assignInputDirectory(Optional<Path>) - Method in class InputArguments
-
Sets an input-directory.
- assignLogger(Logger) - Method in class OutputterChecked
-
Assigns a logger to the outputter, which is used to output warnings or messages when
outputting.
- assignMaximumIndex(int) - Method in class IncreasingIntegers
-
- assignMaximumIndex(int) - Method in class IncrementingIntegers
-
- assignMaximumIndex(int) - Method in class SequenceType
-
If the sequence-type supports a different maximum-index to that derived from the elements
SequenceType.update(T), this assigns it.
- assignMaximumIndex(int) - Method in class StringsWithoutOrder
-
- assignMaxNumberProcessors(String) - Method in class TaskArguments
-
- Assignment<T> - Interface in org.anchoranalysis.annotation.io.assignment
-
A one-to-one pairing between items in two respective sets.
- AssignmentColorPool - Class in org.anchoranalysis.annotation.io.assignment.generator
-
Different
ColorSchemes that can be used to select colors for paired and unpaired objects.
- AssignmentColorPool(int, ColorScheme) - Constructor for class AssignmentColorPool
-
Creates with a number and colors for the paired objects, and defaults colors for unpaired.
- AssignmentColorPool(int, ColorScheme, ColorScheme, boolean) - Constructor for class AssignmentColorPool
-
- AssignmentGenerator - Class in org.anchoranalysis.annotation.io.assignment.generator
-
Outputs a raster showing an
Assignment on a background.
- AssignmentGenerator(DrawColoredObjects, IntFunction<AssignmentColorPool>, Tuple2<String, String>, boolean) - Constructor for class AssignmentGenerator
-
- AssignMode<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
-
How assignments and other decisions are made in the SimulatedAnnealing optimizaton
- AssignMode() - Constructor for class AssignMode
-
- assignModelDirectory(Path) - Method in class InputArguments
-
- assignName(String) - Method in class ClusterIdentifier
-
Assigns a name for the cluster.
- assignOff() - Method in class Mask
-
Interface that allows assignment of an off state to all or subsets of the voxels.
- assignOff() - Method in class BinaryVoxels
-
Creates an assigner that may set the off state in subsequently specified regions of
the voxels.
- assignOff() - Method in class ObjectMask
-
Assigns the off value to voxels, expecting global coordinates.
- assignOn() - Method in class Mask
-
Interface that allows assignment of an on state to all or subsets of the voxels.
- assignOn() - Method in class BinaryVoxels
-
Creates an assigner that may set the on state in subsequently specified regions of the
voxels.
- assignOn() - Method in class ObjectMask
-
Assigns the on value to voxels, expecting global coordinates.
- assignOutputDirectory(Path) - Method in class OutputPrefixerSettings
-
- AssignOverlappingObjects - Class in org.anchoranalysis.annotation.io.assignment
-
Creates a one-to-one
assignment between two sets of
ObjectMasks.
- AssignOverlappingObjects(FeatureEvaluator<FeatureInputPairObjects>, boolean) - Constructor for class AssignOverlappingObjects
-
- assignParentDirectory(Optional<MutableDirectory>) - Method in class MutableDirectory
-
- assignPath(Path) - Method in class SubdirectoryBase
-
- assignPaths(List<Path>) - Method in class InputArguments
-
- assignPaused(DualMarks) - Method in class DualMarksAnnotation
-
Assigns marks with an overall paused state.
- AssignPermutationException - Exception in org.anchoranalysis.bean.permute.assign
-
When the assignment of a permuted value to a property cannot succeed.
- AssignPermutationException(String) - Constructor for exception AssignPermutationException
-
Create with an error message.
- assignPrevious(double, int) - Method in class UnchangedBase
-
Assigns the previous value to be remembered for comparison next time.
- assignPrevious(double, int) - Method in class UnchangedScore
-
- assignPrevious(double, int) - Method in class UnchangedSize
-
- AssignPriority - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
- AssignPriority() - Constructor for class AssignPriority
-
- assignPriority(ObjectVertex, ObjectVertex, GraphLogger) - Method in class AssignPriority
-
Assigns a priority to a potential merge
- AssignPriorityFromImprovement - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
Allows merges if there is an increase in the payload i.e.
- AssignPriorityFromImprovement(PayloadCalculator) - Constructor for class AssignPriorityFromImprovement
-
- AssignPriorityFromPair - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
Calculates pair-feature on each potential merge, and this value determines priority..
- AssignPriorityFromPair(FeatureCalculatorSingle<FeatureInputPairObjects>, double, DoubleBiPredicate) - Constructor for class AssignPriorityFromPair
-
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriority
-
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriorityFromImprovement
-
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class AssignPriorityFromPair
-
- assignProposal(OptimizationStep<S, T, U>, TransformationContext, KernelWithIdentifier<S, U>) - Method in interface KernelAssigner
-
- assignProposal(Optional<T>, KernelWithIdentifier<S, V>) - Method in class OptimizationStep
-
- assignProposal(OptimizationStep<S, T, U>, TransformationContext, KernelWithIdentifier<S, U>) - Method in class KernelAssignerAddErrorLevel
-
- assignProposal(OptimizationStep<S, T, V>, TransformationContext, KernelWithIdentifier<S, V>) - Method in class KernelAssignerCalculateEnergyFromKernel
-
- assignRejected(DualMarks, T) - Method in class DualMarksAnnotation
-
Assigns marks with an overall rejected state.
- assignRelativeForIdentifier() - Method in class InputArguments
-
- assignResolution(Optional<Resolution>) - Method in class Channel
-
Assigns a new resolution.
- assignResolution(Resolution) - Method in class Stack
-
Assigns a new resolution.
- assignShuffle() - Method in class InputArguments
-
- assignSize(String) - Method in class TaskArguments
-
- assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class OutputArguments
-
- assignSuggestedImageOutputFormat(ImageFileFormat) - Method in class OutputPrefixerSettings
-
- assignTaskName(Optional<String>) - Method in class TaskArguments
-
- assignTo(Feature<FeatureInput>) - Method in class Feature
-
Copies fields in this (base) class to target.
- assignTo(KernelPosNeg<T, S>) - Method in class KernelPosNeg
-
Copies fields in this (base) class to target.
- assignTo(ConicFitterBase) - Method in class ConicFitterBase
-
Copies fields in this (base) class to target.
- assignType(String) - Method in class ManifestDescription
-
Assigns a new type.
- assignValue(AnchorBean<?>, Object) - Method in interface PermutationAssigner
-
Assigns value to one or more properties in bean.
- assignValue(int) - Method in class Channel
-
Interface that allows assignment of a particular value to all or subsets of the voxels.
- assignValue(int) - Method in class BoundedVoxels
-
Assigns a value to a bounded-voxels accepting global coordinates for objects, boxes
etc.
- assignValue(int) - Method in class Voxels
-
Interface that allows assignment of a particular value to all or subsets of the voxels.
- assignValue(int) - Method in class VoxelsFloat
-
- assignValue(int) - Method in class VoxelsUnsignedByte
-
- assignValue(int) - Method in class VoxelsUnsignedInt
-
- assignValue(int) - Method in class VoxelsUnsignedShort
-
- assignValue(int) - Method in class VoxelsUntyped
-
Interface that allows assignment of a particular value to all or subsets of the voxels.
- AssignValue - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
Assigns a constant (scalar) value to the portion of the image covered by a mask
- AssignValue() - Constructor for class AssignValue
-
- assignWithPrefix(Feature<? extends FeatureInput>, String, String) - Static method in class AssignFeatureNameUtilities
-
Assigns a new custom-name to a feature, by combining an existing-name with a prefix.
- AsSingle - Class in org.anchoranalysis.mpp.feature.bean.energy.element
-
- AsSingle() - Constructor for class AsSingle
-
- AsSingleMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- AsSingleMark() - Constructor for class AsSingleMark
-
- associated - Variable in class AddOptionsFromCommandLine
-
An associated entity which consumers accept.
- associatedFile() - Method in class AnnotationWithStrategy
-
The file associated with the annotation, if such a file exists.
- AssociatedIndex - Interface in org.anchoranalysis.core.index
-
Associated an index with the object.
- associateFileWithCluster(File, long, ClusterIdentifier) - Method in class ClusterMembership
-
Indicates a particular file is a member of a particular cluster.
- associateXML(XMLConfiguration) - Method in interface AssociateXMLUponLoad
-
Associated an XML configuration with an object.
- associateXML(XMLConfiguration) - Method in class Experiment
-
- associateXML(XMLConfiguration) - Method in class QuickMultiDatasetStructuredExperiment
-
- AssociateXMLUponLoad - Interface in org.anchoranalysis.bean.xml
-
For classes that wish to have a XmlConfiguration associated with them.
- asStack() - Method in class EnergyStack
-
Derive a
Stack representation containing the identical channels to the current
instance.
- asStack() - Method in class EnergyStackWithoutParameters
-
Derive a
Stack representation containing the identical channels to the current
instance.
- asStack() - Method in class RGBStack
-
Exposes the underlying stack, storing the three RGB channels in respective order.
- asTuple() - Method in class Extent
-
Exposes the extent as a tuple.
- asVector3d() - Method in class DirectionVector
-
- at(int, int, int, int) - Static method in class BoundingBoxFactory
-
Short-hand factory method for creating a 2D bounding-box.
- at(int, int, int, int, int, int) - Static method in class BoundingBoxFactory
-
Short-hand factory method for creating a 3D bounding-box.
- atanHandlingNan(double) - Static method in class EllipseStandardFormConverter
-
- atBorder(Extent) - Method in class BoundingBox
-
Does the bounding-box have an edge at the border of an image of size extent?
- AtBorderBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
-
- AtBorderBase() - Constructor for class AtBorderBase
-
- AtBorderXY - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
-
- AtBorderXY() - Constructor for class AtBorderXY
-
- atBorderXY(Extent) - Method in class BoundingBox
-
- AtBorderZ - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
-
- AtBorderZ() - Constructor for class AtBorderZ
-
- atBorderZ(Extent) - Method in class BoundingBox
-
- atCorner(ReadableTuple3i, VoxelsExtracter<T>) - Static method in class VoxelsExtracterFactory
-
- AtIndex - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Creates a new object-collection with only a single element (at a particular index) in the
existing collection.
- AtIndex() - Constructor for class AtIndex
-
- AtLeastZSlices - Class in org.anchoranalysis.plugin.io.bean.file.group.check
-
- AtLeastZSlices() - Constructor for class AtLeastZSlices
-
- AtScale - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Perform a segmentation at a different scale, and then fit the results back to the original scale.
- AtScale() - Constructor for class AtScale
-
- attachObject(Channel) - Method in class MaxIntensity
-
- attachObject(S) - Method in interface ChannelConverterAttached
-
Associate the convert with a particular object.
- attachObject(Histogram) - Method in class MaxIntensityFromHistogram
-
- attachObject(Histogram) - Method in class QuantileIntensityFromHistogram
-
- attachObject(Histogram) - Method in class UpperLowerQuantileIntensityFromHistogram
-
- AutoLocalThreshold - Class in org.anchoranalysis.plugin.fiji.bean.mask.provider
-
Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
- AutoLocalThreshold() - Constructor for class AutoLocalThreshold
-
- Autoname - Class in org.anchoranalysis.plugin.io.bean.channel.map
-
Names of the channels from the metadata if it exists, or after RGB, or by index.
- Autoname() - Constructor for class Autoname
-
- Axis - Enum in org.anchoranalysis.spatial.axis
-
- AxisAlignedUnitVector - Class in org.anchoranalysis.image.bean.spatial.direction
-
- AxisAlignedUnitVector() - Constructor for class AxisAlignedUnitVector
-
- AxisConversionException - Exception in org.anchoranalysis.spatial.axis
-
When converting another type to a corresponding
Axis fails.
- AxisConversionException(String) - Constructor for exception AxisConversionException
-
Create with a messsage, without an underlying cause.
- AxisConverter - Class in org.anchoranalysis.spatial.axis
-
Converts to/from
Axis to a
String and
int representations, checking for
invalid input.
- AxisLimits - Class in org.anchoranalysis.plot
-
- AxisLimits() - Constructor for class AxisLimits
-
- AxisLimits(double, double) - Constructor for class AxisLimits
-
- AxisRatioEllipsoid - Class in org.anchoranalysis.plugin.points.bean.feature
-
- AxisRatioEllipsoid() - Constructor for class AxisRatioEllipsoid
-
- cache(Supplier<T>) - Static method in class CachedSupplier
-
- cache(StoreSupplier<T>) - Static method in interface StoreSupplier
-
Memoizes (caches) the supplied object, and returning it with an identical interface.
- cache(CheckedProgressingSupplier<T, E>) - Static method in class CachedProgressingSupplier
-
- cache(FeatureCalculatorSingle<T>) - Static method in class FeatureCalculatorCache
-
- cache(FeatureCalculatorSingle<T>, int) - Static method in class FeatureCalculatorCache
-
- cache(FeatureCalculatorMulti<T>) - Static method in class FeatureCalculatorCache
-
- cache(FeatureCalculatorMulti<T>, int) - Static method in class FeatureCalculatorCache
-
- cache(NamedStacksSupplier) - Static method in interface NamedStacksSupplier
-
- cache(SerializedObjectSupplier<T>) - Static method in interface SerializedObjectSupplier
-
- CACHE_NAME_FIRST - Static variable in class FeatureDeriveFromPair
-
- CACHE_NAME_MERGED - Static variable in class FeatureDeriveFromPair
-
- CACHE_NAME_SECOND - Static variable in class FeatureDeriveFromPair
-
- CacheAndReuseStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.replace
-
Reuse (without needing to invalidate) an existing session-input as stored in a least-recently
used cache, otherwise create a new one.
- CacheAndReuseStrategy(CacheCreator) - Constructor for class CacheAndReuseStrategy
-
- cacheChecked(CheckedSupplier<T, E>) - Static method in class CachedSupplier
-
- CacheCreator - Interface in org.anchoranalysis.feature.calculate.cache
-
- CachedProgressingSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.progress
-
- CachedSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.cache
-
- CachedSupplierBase<T> - Class in org.anchoranalysis.core.cache
-
Base class for functions that memoize (cache) a call to an interface.
- CachedSupplierBase() - Constructor for class CachedSupplierBase
-
- cacheName() - Method in class DerivedObject
-
- cacheName() - Method in class Erode
-
- cacheName() - Method in class Shell
-
- cacheResettable(StoreSupplier<T>) - Static method in interface StoreSupplier
-
Memoizes (caches) the supplied object, and returning it with a
CachedSupplier
interface
- cachesToAvoidInvalidating() - Method in class CheckCacheForSpecificChildren
-
- cachesToAvoidInvalidating() - Method in interface ChildCacheFinder
-
If set, these particular-caches are exceptionall NOT invalidated during the typical
invalidation operation on their parent.
- cachesToAvoidInvalidating() - Method in class DefaultChildCacheFinder
-
- CacheSupplier<T extends FeatureInput,E extends Exception> - Interface in org.anchoranalysis.feature.session.cache.finder
-
- CacheTransferSource<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.cache.finder
-
An existing cache that can be used as a source for child-caches elsewhere.
- CacheTransferSource(CacheSupplier<T, OperationFailedException>, Set<ChildCacheName>) - Constructor for class CacheTransferSource
-
- CacheTransferSourceCollection - Class in org.anchoranalysis.feature.session.cache.finder
-
- CacheTransferSourceCollection() - Constructor for class CacheTransferSourceCollection
-
- calc(FeatureInputMarkCollection) - Method in class FeatureMarkCollection
-
- calc(EnergyMemoList, EnergySchemeWithSharedFeatures, EnergyStackWithoutParameters) - Method in class EnergySavedAll
-
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class FeatureSingleObjectFromShared
-
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class MaskAsSingleObject
-
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class ObjectAggregationBase
-
- calc(FeatureCalculationInput<T>, CalculationPart<U, T>, Function<ResolvedPart<U, T>, CalculateInputFromDelegateOption<S, T, U>>, Feature<S>, ChildCacheName, double) - Static method in class CalculateInputFromDelegateOption
-
Calculates a feature using a cached-calculation as delegate.
- calc(FeatureInputMarkCollection) - Method in class NumberMarks
-
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class AxisRatioEllipsoid
-
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class EllipsoidBase
-
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class Ellipsoidicity
-
- calculate(FeatureCalculationInput<T>) - Method in class Feature
-
Calculates a value for some input.
- calculate(FeatureCalculationInput<T>) - Method in class Constant
-
- calculate(FeatureCalculationInput<T>) - Method in class Reference
-
- calculate(FeatureCalculationInput<T>) - Method in class Sum
-
- calculate(FeatureInputResults) - Method in class Count
-
- calculate(FeatureCalculationInput<FeatureInputResults>) - Method in class FeatureResults
-
- calculate(FeatureInputResults) - Method in class FeatureResults
-
- calculate(FeatureInputResults) - Method in class FeatureResultsStatistic
-
- calculate(T) - Method in interface FeatureCalculatorMulti
-
Calculate the results of the features with a particular input.
- calculate(T, FeatureList<T>) - Method in interface FeatureCalculatorMulti
-
Calculates the results of a subset of the features with a particular input.
- calculate(T, ErrorReporter, boolean) - Method in interface FeatureCalculatorMulti
-
- calculate(T) - Method in class FeatureCalculatorMultiChangeInput
-
- calculate(T, FeatureList<T>) - Method in class FeatureCalculatorMultiChangeInput
-
- calculate(T) - Method in interface FeatureCalculatorSingle
-
Calculate the results of the feature with a particular input.
- calculate(T) - Method in class FeatureCalculatorSingleChangeInput
-
- calculate(T) - Method in class FeatureCalculatorSingleFromMulti
-
- calculate(Feature<S>, S, ChildCacheName) - Method in interface CalculateForChild
-
Calculates a feature in a child-cache.
- calculate(Feature<S>, CalculationPart<S, T>, ChildCacheName) - Method in interface CalculateForChild
-
Calculates a feature in a child-cache using a new input created from a
CalculationPart.
- calculate(ChildCacheName, S, Function<CalculationPartResolver<S>, ResolvedPart<U, S>>) - Method in interface CalculateForChild
-
- calculate(Feature<T>) - Method in interface FeatureCalculationInput
-
Calculates the result of a feature using this input.
- calculate(FeatureList<T>) - Method in interface FeatureCalculationInput
-
Calculates the results of several features using this input.
- calculate(CalculationPart<S, T>) - Method in interface FeatureCalculationInput
-
Calculates a feature-calculation after resolving it against the main cache.
- calculate(ResolvedPart<S, T>) - Method in interface FeatureCalculationInput
-
Calculates a resolved Feature-calculation.
- calculate(Feature<T>, FeatureCalculationInput<T>) - Method in interface FeatureCalculator
-
Calculate the result of feature with a particular input.
- calculate(FeatureList<T>, FeatureCalculationInput<T>) - Method in interface FeatureCalculator
-
Calculates results for a list of features with a particular input, throwing an exception if a
calculation fails.
- calculate(T) - Method in class SequentialSession
-
- calculate(T, FeatureList<T>) - Method in class SequentialSession
-
- calculate(Feature<T>) - Method in class SessionInputSequential
-
- calculate(FeatureList<T>) - Method in class SessionInputSequential
-
- calculate(CalculationPart<S, T>) - Method in class SessionInputSequential
-
- calculate(ResolvedPart<S, T>) - Method in class SessionInputSequential
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ScaleCalculator
-
Calculates a scaling-factor for a source image/entity of particular dimensions.
- calculate(FeatureCalculationInput<FeatureInputImageMetadata>) - Method in class FeatureImageMetadata
-
- calculate(ImageMetadata) - Method in class FeatureImageMetadata
-
- calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class FeatureHistogramStatistic
-
- calculate(FeatureCalculationInput<FeatureInputObjectCollection>) - Method in class FeatureObjectCollection
-
- calculate(FeatureInputObjectCollection) - Method in class FeatureObjectCollection
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class First
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Merged
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Minimum
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class RatioFirstToSecond
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Second
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class SubtractSecondFromFirst
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class CenterOfGravity
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class NumberVoxels
-
- calculate(FeatureCalculationInput<T>) - Method in class WithResolutionBase
-
- calculate(int[]) - Method in class VoxelScore
-
- calculate(FeatureInputPairObjects) - Method in class PairsTableCalculator
-
- calculate(FeatureInputPairObjects, FeatureList<FeatureInputPairObjects>) - Method in class PairsTableCalculator
-
- calculate(FeatureInputSingleObject) - Method in class SingleTableCalculator
-
- calculate(FeatureInputSingleObject, FeatureList<FeatureInputSingleObject>) - Method in class SingleTableCalculator
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class AsSingle
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class FeatureSingleMemo
-
- calculate(FeatureCalculationInput<FeatureInputMarkCollection>) - Method in class FeatureMarkCollection
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class FeatureMark
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ConstantScaleFactor
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class FitTo
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class Invert
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class MinimumXYResolution
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToDimensions
-
- calculate(Optional<Dimensions>, Optional<ImageSizeSuggestion>) - Method in class ToSuggested
-
- calculate(FeatureCalculationInput<T>) - Method in class FromDimensionsBase
-
- calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class LevelFromHistogram
-
- calculate(FeatureCalculationInput<FeatureInputHistogram>) - Method in class ThresholdHistogram
-
- calculate(ImageMetadata) - Method in class BitDepthPerChannel
-
- calculate(ImageMetadata) - Method in class NumberChannels
-
- calculate(ImageMetadata) - Method in class NumberFrames
-
- calculate(FeatureInputObjectCollection) - Method in class NumberObjects
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class Intersection
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class CostOverlapWithinMidpointDistance
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class OverlapRelative
-
- calculate(FeatureCalculationInput<FeatureInputPairObjects>) - Method in class TouchingVoxels
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ArbitraryInsidePoint
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class AtBorderBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class BoundingBoxAlongAxisBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class BoundingBoxNumberVoxels
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class SpecificEnergyChannelBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class FeatureEnergyChannel
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class GradientMagnitude
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class GradientMeanForAxis
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ImageMomentsBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class DerivedObject
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class NumberRemovedVoxelsAfterClosing
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class OutlineKernelBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ObjectRadiusStandardDeviation
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ShapeRegularityCenterSlice
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class ShapeRegularityMIP
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class FeatureIntersectingObjects
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class PairedWithMask
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class MaximumNumberContourVoxelsOnSlice
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class MaximumNumberVoxelsOnSlice
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class SurfaceNumberVoxelsBase
-
- calculate(int[]) - Method in class Difference
-
- calculate(int[]) - Method in class Identity
-
- calculate(int[]) - Method in class IdentityImposeValueRelationToHistogram
-
- calculate(int[]) - Method in class OutsideRange
-
- calculate(int[]) - Method in class RejectIfIntensityLessThan
-
- calculate(int[]) - Method in class SingleChannel
-
- calculate(FeatureCalculationInput<T>) - Method in class FeatureSingleObjectFromShared
-
- calculate(FeatureCalculationInput<T>) - Method in class ParamFromCollection
-
- calculate(FeatureCalculationInput<T>) - Method in class DataTypeMaxIntensity
-
- calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class Intensity
-
- calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class NumberChannels
-
- calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class AsObjectMask
-
- calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class QuantileAcrossConnectedComponents
-
- calculate(ObjectMask) - Method in interface PayloadCalculator
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class FeatureMarkDirection
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class EccentricityAxisAligned
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class MaxRatioRadii
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class OrderedRadius
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class RadiiRatio
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class BoundingBoxExtent
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class MarkEllipseCircumEstimate
-
- calculate(FeatureCalculationInput<FeatureInputMark>) - Method in class Volume
-
- calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class AsCollection
-
- calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class AsSingleMark
-
- calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class CoefficientOfVarianceFromAll
-
- calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class MeanFromAll
-
- calculate(FeatureCalculationInput<FeatureInputAllMemo>) - Method in class NumberMarks
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class AsMark
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class AsObject
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class BBoxRatio
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class Intensity
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class MaxSliceArea
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class MeanIntensityDifference
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class Size
-
- calculate(FeatureCalculationInput<FeatureInputSingleMemo>) - Method in class SurfaceSizeMaskNonZero
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class BoundingBoxZDistance
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class BoundingBoxZOverlapRatio
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MinimumDistanceByDimension
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class FeatureAsIndividualProportionate
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MinFeatureAsIndividual
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class MaxOverlapRatio
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapNumberVoxelsMask
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapNumVoxels
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapRatio
-
- calculate(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapRatioMask
-
- calculate(FeatureCalculationInput<FeatureInputStack>) - Method in class HOGFeature
-
- calculate(FeatureCalculationInput<T>) - Method in class AbsoluteValue
-
- calculate(FeatureCalculationInput<T>) - Method in class Divide
-
- calculate(FeatureCalculationInput<T>) - Method in class InvertedMax
-
- calculate(FeatureCalculationInput<T>) - Method in class Multiply
-
- calculate(FeatureCalculationInput<T>) - Method in class IfCondition
-
- calculate(FeatureCalculationInput<T>) - Method in class FromDictionary
-
- calculate(FeatureCalculationInput<T>) - Method in class Maximum
-
- calculate(FeatureCalculationInput<T>) - Method in class Mean
-
- calculate(FeatureCalculationInput<T>) - Method in class MeanGeometric
-
- calculate(FeatureCalculationInput<T>) - Method in class Minimum
-
- calculate(FeatureCalculationInput<T>) - Method in class NormalizedRange
-
- calculate(FeatureCalculationInput<T>) - Method in class Range
-
- calculate(FeatureCalculationInput<T>) - Method in class RangeCompareBase
-
- calculate(FeatureCalculationInput<T>) - Method in class StatisticalBase
-
- calculate(FeatureCalculationInput<T>) - Method in class WithValueBase
-
- calculate(FeatureCalculationInput<T>) - Method in class ConvertUnits
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class EllipsoidBase
-
- calculate(FeatureCalculationInput<FeatureInputSingleObject>) - Method in class Ellipticity
-
- calculate(FeatureCalculationInput<FeatureInput>) - Method in class MockFeatureWithCalculation
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class Kernel
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelBirth
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelBirthAndKill
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelDeath
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelExchange
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksFromPartition
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksProposed
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelInitialMarksVoxelized
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelMerge
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelReplace
-
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class KernelSplit
-
- calculateAcceptanceProbability(Kernel<?, ?>, Optional<T>, T, int, KernelCalculationContext) - Method in class AcceptanceProbabilityCalculator
-
- calculateAndOutput(T, FeatureCalculationContext<S>) - Method in class FeatureSource
-
Processes one input to calculate feature-results and output them to the file-system.
- calculateAndOutput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class SingleRowPerInput
-
- calculateAndOutput(MultiInput, FeatureCalculationContext<FeatureTableCalculator<T>>) - Method in class FromObjects
-
- calculateAt(KernelPointCursor) - Method in class AndKernel
-
- calculateAt(KernelPointCursor) - Method in class BinaryKernel
-
Calculates the boolean at a particular point.
- calculateAt(KernelPointCursor) - Method in class ConditionalKernel
-
- calculateAt(KernelPointCursor) - Method in class CountKernel
-
Calculates the count at a particular point.
- calculateAt(KernelPointCursor) - Method in class BinaryKernelMorphological
-
- calculateCheckInitialized(FeatureCalculationInput<T>) - Method in class Feature
-
Calculates the result of a feature and throws an exception if the feature has not been
initialized.
- calculateConnectedComponentID(Point3i, int) - Method in class EncodedVoxels
-
- calculateContext(MarkFactoryContext) - Method in class OptimizationContext
-
- calculateCornerMax() - Method in class BoundingBox
-
The maximum (right-most) point inside the box.
- calculateCornerMaxExclusive() - Method in class BoundingBox
-
The maximum (right-most) point just outside the box.
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelative
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToFirst
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToMaxVolume
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToMerged
-
- calculateDenominator(FeatureInputPairObjects) - Method in class OverlapRelativeToSecond
-
- calculateDensityRatio(double, double, int) - Method in class AnnealScheme
-
- CalculateDeriveMarkCollectionInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- CalculateDeriveMarkCollectionInput() - Constructor for class CalculateDeriveMarkCollectionInput
-
- CalculateDeriveMarkInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- CalculateDeriveMarkInput() - Constructor for class CalculateDeriveMarkInput
-
- CalculateDeriveObjectInput - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
-
- CalculateDeriveObjectInput(int) - Constructor for class CalculateDeriveObjectInput
-
- CalculateDeriveSingleMemoFromPair - Class in org.anchoranalysis.mpp.feature.bean.energy.element
-
- CalculateDeriveSingleMemoFromPair(boolean) - Constructor for class CalculateDeriveSingleMemoFromPair
-
- CalculateDilation - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateDilationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateDilationMap(boolean) - Constructor for class CalculateDilationMap
-
- CalculateDilationMap(CalculateIncrementalOperationMap) - Constructor for class CalculateDilationMap
-
- calculateEccentricity(double, double) - Static method in class PrincipalAxisEccentricity
-
- CalculateEllipseLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipse
-
- CalculateEllipseLeastSquares() - Constructor for class CalculateEllipseLeastSquares
-
- CalculateEllipsoidLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
-
- CalculateErosion - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateErosionMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- CalculateErosionMap(boolean) - Constructor for class CalculateErosionMap
-
- CalculateErosionMap(CalculateIncrementalOperationMap) - Constructor for class CalculateErosionMap
-
- calculateFeatureByIdentifier(String, FeatureCalculationInput<T>) - Method in interface FeatureSymbolCalculator
-
Searches for a feature that matches a particular identifier.
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputSingleObject>) - Method in class ReportFeatureOnObject
-
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputObjectCollection>) - Method in class ReportFeatureOnObjectCollection
-
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<T>) - Method in class ReportFeatureOnObjectsBase
-
- CalculateFeaturesForObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.feature.calculator
-
- CalculateFeaturesForObjects(CombineObjectsForFeatures<T>, InitializationWithEnergyStack, boolean, FeatureCalculationContext<FeatureTableCalculator<T>>) - Constructor for class CalculateFeaturesForObjects
-
- calculateForAxis(Dimensions, Axis) - Method in class Extent
-
- calculateForAxis(Dimensions, Axis) - Method in class ForSpecificAxis
-
- calculateForAxis(Dimensions, Axis) - Method in class VoxelPhysicalSize
-
- calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class FeatureEnergyChannel
-
- calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class Intensity
-
- calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanMaxSlice
-
- calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class IntensityMeanShellBase
-
- calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject>, Channel) - Method in class TextureScore
-
- CalculateForChild<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
-
Performs calculations using child-caches instead of the main cache
- calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class DotProductOrientationToVector
-
- calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class EllipsoidAxisRatio
-
- calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class EllipsoidMaxAreaIntersectingPlane
-
- calculateForEllipsoid(Ellipsoid, Orientation, Vector3d) - Method in class FeatureMarkDirection
-
- calculateForNewMark(MarksFromPartition, Set<Mark>, KernelCalculationContext) - Method in class KernelBirthPartition
-
- calculateForNewMark(T, Set<Mark>, KernelCalculationContext) - Method in class KernelBirth
-
- calculateForNewMark(VoxelizedMarksWithEnergy, Set<Mark>, KernelCalculationContext) - Method in class KernelBirthVoxelized
-
- calculateForObjects(ObjectCollectionProvider, LabelsForInput) - Method in class CalculateFeaturesForObjects
-
- calculateForObjects(ObjectCollection, EnergyStack, LabelsForInput) - Method in class CalculateFeaturesForObjects
-
Calculates the feature-results for objects, and stores the results.
- calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShell
-
- calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShellBase
-
- calculateForShell(ObjectMask, Channel) - Method in class IntensityMeanShellMaxSlice
-
- calculateForVoxel(int, int) - Method in class CalculateLevel
-
- calculateForVoxel(int, int) - Method in class CalculateLevelBase
-
- calculateForVoxel(int, int) - Method in class DifferenceCalculateLevelStandardDeviation
-
- calculateFromAllMoments(ImageMoments) - Method in class ImageMomentsBase
-
- calculateFromAllMoments(ImageMoments) - Method in class PrincipalAxisEccentricity
-
- calculateFromAllMoments(ImageMoments) - Method in class RatioPrincipalAxisLength
-
- calculateFromAllMoments(ImageMoments) - Method in class SpecificAxisBase
-
- calculateFromDimensions(Dimensions) - Method in class Area
-
- calculateFromDimensions(Dimensions) - Method in class ForSpecificAxis
-
- calculateFromDimensions(Dimensions) - Method in class FromDimensionsBase
-
- calculateFromDimensions(Dimensions) - Method in class Volume
-
- calculateFromSpecificMoment(EigenvalueAndVector) - Method in class PrincipalAxisLength
-
- calculateFromSpecificMoment(EigenvalueAndVector) - Method in class PrincipalAxisOrientation
-
- calculateFromSpecificMoment(EigenvalueAndVector) - Method in class SpecificAxisBase
-
Calculates the result for the specific moment identified by index
- CalculateHistogram - Class in org.anchoranalysis.plugin.image.feature.stack.calculation
-
- CalculateHistogram(int) - Constructor for class CalculateHistogram
-
- CalculateHistogramMasked - Class in org.anchoranalysis.plugin.image.feature.stack.calculation
-
Calculated a histogram for a specific region on a channel, as identified by a mask in another
channel
- CalculateHistogramMasked(int, int) - Constructor for class CalculateHistogramMasked
-
- CalculateIncrementalOperationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
-
- CalculateIncrementalOperationMap(boolean) - Constructor for class CalculateIncrementalOperationMap
-
- CalculateIncrementalOperationMap(CalculateIncrementalOperationMap) - Constructor for class CalculateIncrementalOperationMap
-
- CalculateInputFromDelegate<S,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate
-
A base class for
CalculationParts that derive from an existing "delegate" calculation.
- CalculateInputFromDelegate(CalculationPart<U, T>, CalculationPartResolver<T>) - Constructor for class CalculateInputFromDelegate
-
- CalculateInputFromDelegate(ResolvedPart<U, T>) - Constructor for class CalculateInputFromDelegate
-
- CalculateInputFromDelegateOption<S extends FeatureInput,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate
-
- CalculateInputFromDelegateOption(ResolvedPart<U, T>) - Constructor for class CalculateInputFromDelegateOption
-
Creates with a delegate.
- CalculateInputFromPair - Class in org.anchoranalysis.image.feature.calculation
-
Calculates a single-input from a pair
- CalculateInputFromPair(CalculateInputFromPair.Extract) - Constructor for class CalculateInputFromPair
-
- CalculateInputFromPair.Extract - Enum in org.anchoranalysis.image.feature.calculation
-
- CalculateIntersecting - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
-
- CalculateIntersecting(ResolvedPart<ObjectCollection, FeatureInputSingleObject>, int) - Constructor for class CalculateIntersecting
-
- CalculateLevel - Class in org.anchoranalysis.image.bean.threshold
-
Calculates a threshold-level from a histogram.
- CalculateLevel() - Constructor for class CalculateLevel
-
- calculateLevel(Histogram) - Method in class CalculateLevel
-
Determines a voxel intensity that can be used for thresholding.
- calculateLevel(Histogram) - Method in class CalculateLevelRelativeToThreshold
-
- calculateLevel(Histogram) - Method in class ClampHistogramMax
-
- calculateLevel(Histogram) - Method in class Constant
-
- calculateLevel(Histogram) - Method in class EmptyHistogramConstant
-
- calculateLevel(Histogram) - Method in class Maximum
-
- calculateLevel(Histogram) - Method in class Minimum
-
- calculateLevel(Histogram) - Method in class Otsu
-
- calculateLevel(Histogram) - Method in class OtsuWeighted
-
- calculateLevel(Histogram) - Method in class Quantile
-
- CalculateLevel - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- CalculateLevel() - Constructor for class CalculateLevel
-
- CalculateLevelBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- CalculateLevelBase() - Constructor for class CalculateLevelBase
-
- calculateLevelIncoming(Histogram) - Method in class CalculateLevelOne
-
- CalculateLevelListBase - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
- CalculateLevelListBase() - Constructor for class CalculateLevelListBase
-
- CalculateLevelOne - Class in org.anchoranalysis.image.bean.threshold
-
- CalculateLevelOne() - Constructor for class CalculateLevelOne
-
- CalculateLevelRelativeToThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
- CalculateLevelRelativeToThreshold() - Constructor for class CalculateLevelRelativeToThreshold
-
- calculateMaximum() - Method in class Histogram
-
Calculates the maximum value with non zero-count among the histogram values.
- calculateMaybeSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class PairsTableCalculator
-
- calculateMeanIntensityObject(Channel, ObjectMask) - Static method in class IntensityMeanCalculator
-
- calculateMeanIntensityObject(Channel, ObjectMask, boolean) - Static method in class IntensityMeanCalculator
-
- calculateMidpoint(ObjectWithProperties, boolean) - Static method in class Midpoint
-
- calculateMinimum() - Method in class Histogram
-
Calculates the minimum value with non zero-count among the histogram values.
- calculateMinMax(Optional<Resolution>, boolean) - Method in class MarkBounds
-
- calculateMode() - Method in class Histogram
-
Calculates the mode of the histogram values.
- calculateNewMaxCurrentValue() - Method in class PriorityQueueIndexRangeDownhill
-
- CalculateNumberVoxels - Class in org.anchoranalysis.image.feature.calculation
-
- CalculateNumberVoxels(boolean) - Constructor for class CalculateNumberVoxels
-
- CalculateObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
-
- CalculateObjectMask(CalculateObjectMask) - Constructor for class CalculateObjectMask
-
Copy constructor
- CalculateObjectMask(int, ResolvedPartMap<ObjectMask, FeatureInputSingleObject, Integer>) - Constructor for class CalculateObjectMask
-
- calculateOrientation(ObjectWithProperties) - Static method in class Orientation
-
- CalculateOrientationChange - Interface in org.anchoranalysis.image.io.stack
-
Calculates any needed orientation change.
- calculateOrientationChange(Logger) - Method in interface CalculateOrientationChange
-
Calculates any needed orientation change.
- CalculateOverlap - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlap(int) - Constructor for class CalculateOverlap
-
- CalculateOverlapMask - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMask(int, int, byte) - Constructor for class CalculateOverlapMask
-
- CalculateOverlapMIP - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMIP(int) - Constructor for class CalculateOverlapMIP
-
- CalculateOverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMIPBase(int) - Constructor for class CalculateOverlapMIPBase
-
- CalculateOverlapMIPRatio - Class in org.anchoranalysis.plugin.mpp.feature.overlap
-
- CalculateOverlapMIPRatio(int) - Constructor for class CalculateOverlapMIPRatio
-
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIP
-
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIPBase
-
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class CalculateOverlapMIPRatio
-
- calculatePath() - Method in class MutableDirectory
-
- calculatePath() - Method in class OutputtedFile
-
- calculatePoint(ObjectWithProperties, String) - Static method in class Orientation
-
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class MergeLists
-
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class PointsFromOrientationProposer
-
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class TraversePointsOnContour
-
- calculateResultsForInput(FileInput, FeatureCalculationContext<FeatureList<FeatureInputHistogram>>) - Method in class FromHistogram
-
- calculateResultsForInput(ProvidesStackInput, FeatureCalculationContext<FeatureList<FeatureInputStack>>) - Method in class FromImage
-
- calculateResultsForInput(ImageMetadataInput, FeatureCalculationContext<FeatureList<FeatureInputImageMetadata>>) - Method in class FromImageMetadata
-
- calculateResultsForInput(T, FeatureCalculationContext<FeatureList<S>>) - Method in class SingleRowPerInput
-
Calculates feature-results for a particular input.
- calculateRunningSum(Mask, Voxels<UnsignedByteBuffer>) - Static method in class IterateVoxelsMask
-
Calculates the sum and count across voxels intensity that correspond to on voxels on a
mask
- calculateScaleFactor(Optional<Dimensions>) - Method in interface ImageSizeSuggestion
-
Calculates the scaling factor.
- CalculateShellObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
-
- CalculateShellObjectMask(ResolvedPart<ObjectMask, FeatureInputSingleObject>, ResolvedPart<ObjectMask, FeatureInputSingleObject>, int, boolean, boolean) - Constructor for class CalculateShellObjectMask
-
- calculateSigma(Dimensions, MessageLogger) - Method in class BlurStrategy
-
- calculateStatisticFrom(Histogram) - Method in class FeatureHistogramStatistic
-
Calculates the statistic from the histogram, that is subsequently returned as the
feature-value.
- calculateStatisticFrom(Histogram) - Method in class Mean
-
- calculateStatisticFrom(Histogram) - Method in class CoefficientOfVariation
-
- calculateStatisticFrom(Histogram) - Method in class Count
-
- calculateStatisticFrom(Histogram) - Method in class Kurtosis
-
- calculateStatisticFrom(Histogram) - Method in class Max
-
- calculateStatisticFrom(Histogram) - Method in class MeanRaisedToPower
-
- calculateStatisticFrom(Histogram) - Method in class Median
-
- calculateStatisticFrom(Histogram) - Method in class Min
-
- calculateStatisticFrom(Histogram) - Method in class Mode
-
- calculateStatisticFrom(Histogram) - Method in class NumberDistinctValues
-
- calculateStatisticFrom(Histogram) - Method in class Quantile
-
- calculateStatisticFrom(Histogram) - Method in class Range
-
- calculateStatisticFrom(Histogram) - Method in class RatioNonMode
-
- calculateStatisticFrom(Histogram) - Method in class Skewness
-
- calculateStatisticFrom(Histogram) - Method in class StdDev
-
- calculateStatisticFrom(Histogram) - Method in class Sum
-
- calculateStatisticFrom(Histogram) - Method in class TotalCount
-
- calculateStatisticFrom(Histogram) - Method in class Variance
-
- calculateStatisticFrom(Histogram) - Method in class RatioThreshold
-
- calculateSum() - Method in class Histogram
-
Calculates the sum of all values in the distribution considering their counts.
- calculateSumCubes() - Method in class Histogram
-
Calculates the cube of the squares of all values in the distribution considering their
counts.
- calculateSumSquares() - Method in class Histogram
-
Calculates the sum of the squares of all values in the distribution considering their
counts.
- calculateSuppressErrors(T, ErrorReporter) - Method in interface FeatureCalculatorMulti
-
Calculates the results for an
input recording the error to an
ErrorReporter
if anything goes wrong, but throwing no exception.
- calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorMultiChangeInput
-
- calculateSuppressErrors(T, ErrorReporter) - Method in interface FeatureCalculatorSingle
-
Calculates the result for an
input recording the error to an
ErrorReporter if
anything goes wrong, but throwing no exception.
- calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorSingleChangeInput
-
- calculateSuppressErrors(T, ErrorReporter) - Method in class FeatureCalculatorSingleFromMulti
-
- calculateSuppressErrors(T, ErrorReporter) - Method in class SequentialSession
-
Calculates the next-object in our sequential series, reporting any exceptions into a reporter
log
- calculateSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class PairsTableCalculator
-
- calculateSuppressErrors(FeatureInputSingleObject, ErrorReporter) - Method in class SingleTableCalculator
-
- calculateTemperature(int) - Method in class AnnealScheme
-
- calculateTemperature(int) - Method in class Geometry
-
- calculateTemperature(int) - Method in class NoAnnealing
-
- calculateVolume() - Method in class Dimensions
-
Calculates the volume of the
Extent when considered as a box.
- calculateVolume() - Method in class Extent
-
Calculates the volume of the
Extent when considered as a box.
- calculateVolumeAsInt() - Method in class Extent
-
- calculateWith(Feature<T>, T, Logger) - Static method in class FeatureSession
-
Starts a feature-session for a single feature - and performs a calculation.
- calculateWithChannel(ObjectMask, Channel) - Method in class CountEqual
-
- calculateWithChannel(ObjectMask, Channel) - Method in class SpecificEnergyChannelBase
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class HasTouchingVoxels
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class NumberTouchingVoxelFaces
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class NumberTouchingVoxels
-
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class TouchingVoxels
-
- calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class NumberVoxelsAtBorder
-
- calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class NumberNeighboringVoxels
-
- calculateWithParameters(ObjectMask, KernelApplicationParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class OutlineKernelBase
-
- calculateWithResolution(double, Resolution) - Method in class FeatureConvertUnits
-
- calculateWithResolution(double, Resolution) - Method in class WithResolutionBase
-
- calculateWithResolution(double, Resolution) - Method in class UnitsWithinRange
-
- calculateZScore(double, double, double) - Static method in class ZScoreCalculator
-
Calculates a Z-Score for a particular value and parameterization.
- CalculationPart<S,T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.part
-
A sub-part of the calculation of a feature, that can be cached, and reused by other features.
- CalculationPart() - Constructor for class CalculationPart
-
- CalculationPartMap<S,T extends FeatureInput,U,E extends Exception> - Class in org.anchoranalysis.feature.calculate.part
-
Similar to a
CalculationPart but stores several evaluation results, differentiated by a
key.
- CalculationPartMap(int) - Constructor for class CalculationPartMap
-
Creates for a particular cache-size.
- CalculationPartResolver<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.part
-
- calculationResultsNeeded(MultiLevelOutputEnabled) - Method in class FeatureOutputNames
-
If any output is enabled that requires calculation of feature results?
- calculator() - Method in interface FeatureCalculationCache
-
A means of calculating feature values using this cache.
- calculatorForAll(FeatureList<T>) - Method in class FeatureCalculatorFromProvider
-
Calculates all image-features in the feature-store
- calculatorSingleFromProvider(FeatureListProvider<T>, String) - Method in class FeatureCalculatorFromProvider
-
Calculates a single-feature that comes from a provider (but can reference the other features
from the store)
- call(CheckedSupplier<T, E>) - Method in class CachedSupplierBase
-
Gets the value supplied by supplier via the cache if it exists, or otherwise via the
supplier.
- call() - Method in class CallableJob
-
- CallableJob<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.task.processor
-
A job derived from a
Task that can be placed on different threads
- CallableJob(Task<T, S>, ParametersUnbound<T, S>, JobState, JobDescription, ConcurrentJobMonitor, Optional<MessageLogger>, int) - Constructor for class CallableJob
-
Constructor.
- callEachPointInNeighborhood(Point3i, Neighborhood, boolean, ProcessVoxelNeighbor<T>, int, int) - Static method in class IterateVoxelsNeighbors
-
Iterate over each point in the neighborhood of an existing point.
- canEqual(Object) - Method in class DoubleList
-
- canEqual(Object) - Method in class DoubleSet
-
- canEqual(Object) - Method in class IntegerList
-
- canEqual(Object) - Method in class IntegerSet
-
- canEqual(Object) - Method in class StringList
-
- canEqual(Object) - Method in class StringSet
-
- canEqual(Object) - Method in class RootPath
-
- canEqual(Object) - Method in class EqualToBean
-
- canEqual(Object) - Method in class GreaterThanBean
-
- canEqual(Object) - Method in class GreaterThanEqualToBean
-
- canEqual(Object) - Method in class LessThanBean
-
- canEqual(Object) - Method in class LessThanEqualToBean
-
- canEqual(Object) - Method in class RelationBean
-
- canEqual(Object) - Method in class RelationToConstant
-
- canEqual(Object) - Method in class Indexable
-
- canEqual(Object) - Method in class ChildCacheName
-
- canEqual(Object) - Method in class FeatureInputDimensions
-
- canEqual(Object) - Method in class FeatureInputEnergy
-
- canEqual(Object) - Method in class FeatureInputNull
-
- canEqual(Object) - Method in class SimpleName
-
- canEqual(Object) - Method in class SizeXY
-
- canEqual(Object) - Method in class CalculateLevelOne
-
- canEqual(Object) - Method in class BinaryNotOffVoxels
-
- canEqual(Object) - Method in class BinaryNotOnVoxels
-
- canEqual(Object) - Method in class BinaryOffVoxels
-
- canEqual(Object) - Method in class BinaryOnVoxels
-
- canEqual(Object) - Method in class BinaryVoxelsBase
-
- canEqual(Object) - Method in class CalculateInputFromPair
-
- canEqual(Object) - Method in class CalculateNumberVoxels
-
- canEqual(Object) - Method in class FeatureInputImageMetadata
-
- canEqual(Object) - Method in class FeatureInputObjectCollection
-
- canEqual(Object) - Method in class FeatureInputPairObjects
-
- canEqual(Object) - Method in class FeatureInputSingleObject
-
- canEqual(Object) - Method in class FeatureInputStack
-
- canEqual(Object) - Method in class UnsignedBuffer
-
- canEqual(Object) - Method in class UnsignedBufferAsInt
-
- canEqual(Object) - Method in class UnsignedByteBuffer
-
- canEqual(Object) - Method in class UnsignedIntBuffer
-
- canEqual(Object) - Method in class UnsignedShortBuffer
-
- canEqual(Object) - Method in class QuadraticEquationSolver.QuadraticRoots
-
- canEqual(Object) - Method in class MeanScale
-
- canEqual(Object) - Method in class RegionMap
-
- canEqual(Object) - Method in class RegionMembership
-
- canEqual(Object) - Method in class RegionMembershipWithFlags
-
- canEqual(Object) - Method in class CalculateDeriveSingleMemoFromPair
-
- canEqual(Object) - Method in class FeatureInputMark
-
- canEqual(Object) - Method in class IndexableMarksWithEnergy
-
- canEqual(Object) - Method in class FeatureInputAllMemo
-
- canEqual(Object) - Method in class FeatureInputPairMemo
-
- canEqual(Object) - Method in class FeatureInputSingleMemo
-
- canEqual(Object) - Method in class MemoList
-
- canEqual(Object) - Method in class ColoredMarksWithDisplayStack
-
- canEqual(Object) - Method in class MarksWithDisplayStack
-
- canEqual(Object) - Method in class OverlayMark
-
- canEqual(Object) - Method in class FeedbackBeginParameters
-
- canEqual(Object) - Method in class IndexableOverlays
-
- canEqual(Object) - Method in class AxisLimits
-
- canEqual(Object) - Method in class CalculateLevelListBase
-
- canEqual(Object) - Method in class CalculateLevelRelativeToThreshold
-
- canEqual(Object) - Method in class ClampHistogramMax
-
- canEqual(Object) - Method in class Constant
-
- canEqual(Object) - Method in class EmptyHistogramConstant
-
- canEqual(Object) - Method in class IfGreaterThan
-
- canEqual(Object) - Method in class IfLessThan
-
- canEqual(Object) - Method in class Maximum
-
- canEqual(Object) - Method in class Minimum
-
- canEqual(Object) - Method in class Otsu
-
- canEqual(Object) - Method in class OtsuWeighted
-
- canEqual(Object) - Method in class Quantile
-
- canEqual(Object) - Method in class MorphologicalIterations
-
- canEqual(Object) - Method in class CalculateIntersecting
-
- canEqual(Object) - Method in class CalculateDeriveObjectInput
-
- canEqual(Object) - Method in class CalculateInputFromDelegate
-
- canEqual(Object) - Method in class CalculateInputFromDelegateOption
-
- canEqual(Object) - Method in class CalculateIncrementalOperationMap
-
- canEqual(Object) - Method in class CalculateObjectMask
-
- canEqual(Object) - Method in class CalculateShellObjectMask
-
- canEqual(Object) - Method in class CalculateDilation
-
- canEqual(Object) - Method in class CalculateDilationMap
-
- canEqual(Object) - Method in class CalculateErosion
-
- canEqual(Object) - Method in class CalculateErosionMap
-
- canEqual(Object) - Method in class CalculateHistogram
-
- canEqual(Object) - Method in class CalculateHistogramMasked
-
- canEqual(Object) - Method in class ChangeableOutputSequence
-
- canEqual(Object) - Method in class SortedSetChannel
-
- canEqual(Object) - Method in class SortedSetSlice
-
- canEqual(Object) - Method in class AllSlicesMaskEverythingNonZero
-
- canEqual(Object) - Method in class AllSlicesMaskNonZero
-
- canEqual(Object) - Method in class CenterSlice
-
- canEqual(Object) - Method in class CenterSliceBase
-
- canEqual(Object) - Method in class CenterSliceWindow
-
- canEqual(Object) - Method in class GreatestAreaSlice
-
- canEqual(Object) - Method in class IndexedRegionBase
-
- canEqual(Object) - Method in class SelectSlicesBase
-
- canEqual(Object) - Method in class SelectSlicesWithIndexBase
-
- canEqual(Object) - Method in class Specific
-
- canEqual(Object) - Method in class CalculateDeriveMarkCollectionInput
-
- canEqual(Object) - Method in class CalculateDeriveMarkInput
-
- canEqual(Object) - Method in class CalculateOverlap
-
- canEqual(Object) - Method in class CalculateOverlapMask
-
- canEqual(Object) - Method in class CalculateOverlapMIP
-
- canEqual(Object) - Method in class CalculateOverlapMIPBase
-
- canEqual(Object) - Method in class CalculateOverlapMIPRatio
-
- canEqual(Object) - Method in class HOGParameters
-
- canEqual(Object) - Method in class FitResult
-
- canEqual(Object) - Method in class CalculateEllipseLeastSquares
-
- canEqual(Object) - Method in class CalculateEllipsoidLeastSquares
-
- canEqual(Object) - Method in class Orientation2D
-
- canEqual(Object) - Method in class Orientation3DEulerAngles
-
- canEqual(Object) - Method in class OrientationAxisAngle
-
- canEqual(Object) - Method in class OrientationRotationMatrix
-
- canEqual(Object) - Method in class Point3d
-
- canEqual(Object) - Method in class Point3f
-
- canEqual(Object) - Method in class Point3i
-
- canEqual(Object) - Method in class Tuple3d
-
- canEqual(Object) - Method in class Tuple3f
-
- canEqual(Object) - Method in class Tuple3i
-
- canEqual(Object) - Method in class Vector3d
-
- canExceptionBeCombined(Throwable) - Method in exception BeanMisconfiguredXMLException
-
- canExceptionBeCombined(Throwable) - Method in exception LocalisedBeanException
-
- canExceptionBeCombined(Throwable) - Method in exception AnchorCombinableException
-
Can another exception be combined with this exception?
- canExceptionBeCombined(Throwable) - Method in exception NamedProviderGetException
-
- canExceptionBeSkipped(Throwable) - Method in exception BeanMisconfiguredXMLException
-
- canExceptionBeSkipped(Throwable) - Method in exception LocalisedBeanException
-
- canExceptionBeSkipped(Throwable) - Method in exception AnchorCombinableException
-
Can another exception be skipped, when we combine with the current exception?
- canExceptionBeSkipped(Throwable) - Method in exception NamedProviderGetException
-
- canValueRangeChange() - Method in class Interpolator
-
Returns true if it's possible for values to be created after interpolation that aren't found
in the input-image.
- canValueRangeChange() - Method in class InterpolatorImgLib2Lanczos
-
- canValueRangeChange() - Method in class InterpolatorImgLib2Linear
-
- canValueRangeChange() - Method in class InterpolatorImgLib2NearestNeighbor
-
- canValueRangeChange() - Method in class InterpolatorNone
-
- canValueRangeChange() - Method in class InterpolatorRecordExecutionTime
-
- canValueRangeChange() - Method in class InterpolatorImageJ
-
- canValueRangeChange() - Method in class InterpolatorOpenCV
-
- capacity() - Method in class UnsignedBuffer
-
- capacity() - Method in class VoxelBuffer
-
The capacity (i.e.
- capacity() - Method in class VoxelBufferUnsigned
-
- castAs() - Method in class Feature
-
Casts the feature to having a different input-type.
- Cell - Class in org.anchoranalysis.image.bean.spatial.arrange
-
- Cell() - Constructor for class Cell
-
- CenterOfGravity - Class in org.anchoranalysis.image.feature.bean.object.single
-
- CenterOfGravity(Axis) - Constructor for class CenterOfGravity
-
Creates for a specific axis.
- CenterOfGravity() - Constructor for class CenterOfGravity
-
- centerOfGravity() - Method in class ObjectMask
-
Calculates center-of-gravity across all axes.
- centerOfGravity(Axis) - Method in class ObjectMask
-
Calculates center-of-gravity for one specific axis only.
- centerOfGravity() - Method in class BoundingBox
-
A mid-point in the bounding-box, corresponding to the mean of all points inside the box.
- CenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
-
- CenterOnMask() - Constructor for class CenterOnMask
-
- centerPoint() - Method in class Mark
-
- centerPoint() - Method in class MarkWithPosition
-
- centerPoint() - Method in class LineSegment
-
- centerPoint() - Method in class PointList
-
- centerPoint() - Method in class Polygon
-
- centerPoint() - Method in class PolygonCurve
-
- centerPoint() - Method in class EllipseStandardFormConverter
-
- CenterSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- CenterSlice() - Constructor for class CenterSlice
-
- CenterSliceBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- CenterSliceBase() - Constructor for class CenterSliceBase
-
- CenterSliceWindow - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Like {#link org.anchoranalysis.plugin.mpp.bean.region.CenterSlice} but considers more than one
slice, specifically centerSlice+- windowSize
- CenterSliceWindow() - Constructor for class CenterSliceWindow
-
- chainCode(int, int, int) - Static method in class ChainCodesDirection
-
- chainCodes(int) - Method in class WatershedEncoding
-
Decodes a chain-code into a point
- ChainCodesDirection - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
-
Maps directions to chain codes
- ChangeableOutputSequence<T,S> - Class in org.anchoranalysis.plugin.image.task.bean.format
-
- ChangeableOutputSequence() - Constructor for class ChangeableOutputSequence
-
- changedMarkIDArray() - Method in class Kernel
-
The mark ids that were changed in the last energy calculation for the kernel
- changedMarkIDArray() - Method in class KernelBirth
-
- changedMarkIDArray() - Method in class KernelBirthAndKill
-
- changedMarkIDArray() - Method in class KernelDeath
-
- changedMarkIDArray() - Method in class KernelExchange
-
- changedMarkIDArray() - Method in class KernelInitialMarksFromPartition
-
- changedMarkIDArray() - Method in class KernelInitialMarksProposed
-
- changedMarkIDArray() - Method in class KernelInitialMarksVoxelized
-
- changedMarkIDArray() - Method in class KernelMerge
-
- changedMarkIDArray() - Method in class KernelReplace
-
- changedMarkIDArray() - Method in class KernelSplit
-
- changedOffset(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
Calculates the offset in the buffer for a voxel, indicated by its relative-change in
position.
- changeExtension(Path, NonImageFileFormat, FileFormat) - Static method in class FormatExtensions
-
Change the extension in a path.
- changeExtent(Extent) - Method in class BoundingBox
-
Creates a copied
BoundingBox but with a different extent.
- changeExtentZ(int) - Method in class BoundingBox
-
Creates a copied
BoundingBox but with a different extent in the Z-dimension.
- changeInput(U) - Method in class InputBound
-
Immutably changes the input-object
- changeInputAndSharedState(U, V) - Method in class InputBound
-
Immutably changes the input-object and shared-state
- changeIntensity(Voxels<?>, IntUnaryOperator) - Static method in class IterateVoxelsAll
-
Changes each voxel, reading and writing the buffer as an int.
- changePrefix(DirectoryWithPrefix) - Method in class OutputterTarget
-
- changePrefix(DirectoryWithPrefix, Optional<WriteOperationRecorder>) - Method in class OutputterChecked
-
- changeZ(int, int) - Method in class BoundingBox
-
Creates a copied
BoundingBox but with a different corner and extent in the
Z-dimension.
- Channel - Class in org.anchoranalysis.image.core.channel
-
A channel from an image.
- Channel(Voxels<?>, Optional<Resolution>) - Constructor for class Channel
-
Creates for particular voxels and resolution.
- channel() - Method in class Mask
-
The underlying channel which contains the binary-values.
- channel(String) - Static method in class ReferenceFactory
-
- ChannelConverter<T> - Class in org.anchoranalysis.image.core.channel.convert
-
Base class to convert
Channels from one type to another specific type.
- ChannelConverter(VoxelDataType, VoxelsConverter<T>, VoxelsFactoryTypeBound<T>) - Constructor for class ChannelConverter
-
- ChannelConverterAttached<S,T> - Interface in org.anchoranalysis.image.core.channel.convert.attached
-
A channel-converter that has been permanently associated with a particular object.
- ChannelConverterMulti - Class in org.anchoranalysis.image.core.channel.convert
-
Converts a channel from one voxel data-type to one of multiple other types.
- ChannelConverterMulti() - Constructor for class ChannelConverterMulti
-
- ChannelConvertStyle - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Converts a channel(s) at a particular timepoint into a stack(s).
- ChannelConvertStyle() - Constructor for class ChannelConvertStyle
-
- ChannelEntry - Class in org.anchoranalysis.image.io.bean.channel
-
- ChannelEntry(String, int) - Constructor for class ChannelEntry
-
- ChannelFactory - Class in org.anchoranalysis.image.core.channel.factory
-
Creates a
Channel corresponding to one of several data-types.
- ChannelFactoryFloat - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryFloat() - Constructor for class ChannelFactoryFloat
-
Default constructor.
- ChannelFactorySingleType - Class in org.anchoranalysis.image.core.channel.factory
-
Creates a
Channel for a specific data-type.
- ChannelFactorySingleType(VoxelDataType, VoxelsFactoryTypeBound<?>) - Constructor for class ChannelFactorySingleType
-
- ChannelFactoryUnsignedByte - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryUnsignedByte() - Constructor for class ChannelFactoryUnsignedByte
-
Default constructor.
- ChannelFactoryUnsignedInt - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryUnsignedInt() - Constructor for class ChannelFactoryUnsignedInt
-
Default constructor.
- ChannelFactoryUnsignedShort - Class in org.anchoranalysis.image.core.channel.factory
-
- ChannelFactoryUnsignedShort() - Constructor for class ChannelFactoryUnsignedShort
-
Default constructor.
- ChannelFilter - Class in org.anchoranalysis.image.io.bean.channel
-
Applies a filter to a particular channel
- ChannelFilter() - Constructor for class ChannelFilter
-
- ChannelGenerator - Class in org.anchoranalysis.image.io.channel.output
-
Writes a single channel to a file.
- ChannelGenerator(String) - Constructor for class ChannelGenerator
-
- ChannelGetter - Interface in org.anchoranalysis.image.io.channel.input
-
- ChannelGetterForTimepoint - Class in org.anchoranalysis.plugin.image.task.stack
-
- ChannelGetterForTimepoint(ChannelGetter, int) - Constructor for class ChannelGetterForTimepoint
-
- ChannelMap - Class in org.anchoranalysis.image.io.bean.channel
-
- ChannelMap() - Constructor for class ChannelMap
-
- ChannelMapper - Class in org.anchoranalysis.image.core.stack
-
Helps retrieve channel and an associated converter and apply operation on them jointly.
- ChannelMapper(IntFunction<Channel>, IntFunction<Optional<ChannelConverterAttached<Channel, UnsignedByteBuffer>>>) - Constructor for class ChannelMapper
-
- channelNames() - Method in interface NamedChannelsForSeries
-
- channelNames() - Method in class NamedChannelsForSeriesConcatenate
-
- channelNames() - Method in class NamedChannelsForSeriesMap
-
- channelNames(Logger) - Method in interface OpenedImageFile
-
The names of each channel, if they are known.
- channelNames(Logger) - Method in class OpenedMultiFile
-
- ChannelProvider - Class in org.anchoranalysis.image.bean.provider
-
- ChannelProvider() - Constructor for class ChannelProvider
-
- ChannelProviderBinary - Class in org.anchoranalysis.image.bean.provider
-
A channel-provider based-on two input channel-providers that must be of the same dimensionality
- ChannelProviderBinary() - Constructor for class ChannelProviderBinary
-
- ChannelProviderTernary - Class in org.anchoranalysis.image.bean.provider
-
- ChannelProviderTernary() - Constructor for class ChannelProviderTernary
-
- ChannelProviderUnary - Class in org.anchoranalysis.image.bean.provider
-
- ChannelProviderUnary() - Constructor for class ChannelProviderUnary
-
- channels() - Method in class ImageInitialization
-
- ChannelSource - Class in org.anchoranalysis.plugin.image.task.grouped
-
Source of channels for aggregating.
- ChannelSource(NamedStacks, ConsistentChannelChecker, Optional<SizeXY>) - Constructor for class ChannelSource
-
- channelsPerByteArray(IFormatReader) - Method in class Default
-
- channelsPerByteArray(IFormatReader) - Method in class ForceChannelsPerByteArray
-
- channelsPerByteArray(IFormatReader) - Method in class ReadOptions
-
The number of channels returned with each call to IFormatReader.openBytes(int).
- channelsPerByteArray(IFormatReader) - Method in class ReadOptionsDelegate
-
- check(Mark, RegionMap, EnergyStack) - Method in class CheckMark
-
Checks a mark
- check(Channel, Mask) - Static method in class DimensionsChecker
-
- check(Channel, String, Dimensions) - Static method in class DimensionsChecker
-
Checks a channel to make sure it's the same size as an an existing channel
- check(Mask, String, Dimensions) - Static method in class DimensionsChecker
-
Checks a channel to make sure it's the same size as an an existing channel
- check(Mark, RegionMap, EnergyStack) - Method in class AndList
-
- check(Mark, RegionMap, EnergyStack) - Method in class AnySliceCenterOnMask
-
- check(Mark, RegionMap, EnergyStack) - Method in class CenterOnMask
-
- check(Mark, RegionMap, EnergyStack) - Method in class FeatureValueCheckMark
-
- check(Mark, RegionMap, EnergyStack) - Method in class Not
-
- check(Mark, RegionMap, EnergyStack) - Method in class RadiiMinRatio
-
- check(Mark, RegionMap, EnergyStack) - Method in class VolumeMin
-
- Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- Check() - Constructor for class Check
-
- Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
-
- Check() - Constructor for class Check
-
- check(T) - Static method in class BeanTestChecker
-
Checks if a bean has all necessary items, throwing a run-time exception if it does not.
- checkAbsolutePath() - Method in class OutputPrefixerSettings
-
- checkAndInit(T, P, Logger) - Static method in class BeanTestChecker
-
- CheckCacheForSpecificChildren - Class in org.anchoranalysis.feature.session.cache.finder
-
For particular child-caches, check if a session-input is available from another LRU-cache and
reuse.
- CheckCacheForSpecificChildren(Class<?>, CacheTransferSourceCollection) - Constructor for class CheckCacheForSpecificChildren
-
- checkChannelType(VoxelDataType) - Method in class ConsistentChannelChecker
-
Checks that a channel has the same type (max value) as the others
- checkCompatibleWith(Mark) - Method in class KernelProposer
-
- CheckedBiConsumer<S,T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
BiConsumer but can also throw a checked exception.
- CheckedBiFunction<S,T,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
BiFunction but can also throw a checked exception.
- CheckedBooleanSupplier<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedConsumer<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Consumes a value and throws an exception.
- CheckedFunction<S,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Function but can also thrown an exception.
- CheckedIntConsumer<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Consumes an int and throws an exception.
- CheckedIntFunction<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedPredicate<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Predicate but can also throw an exception.
- CheckedProgressingSupplier<R,E extends Exception> - Interface in org.anchoranalysis.core.progress
-
Like
CheckedSupplier but can update a progress-reporter as the operation progresses.
- CheckedRunnable<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Runnable but can also throw an exception.
- CheckedStream - Class in org.anchoranalysis.core.functional
-
Map operations for streams that can throw checked-exceptions.
- CheckedStream.ConvertedToRuntimeException - Exception in org.anchoranalysis.core.functional
-
An exception that wraps another exception, but exposes itself as a
RuntimeException.
- CheckedSupplier<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Supplier but can also throw an exception.
- CheckedToDoubleBiFunction<T,U,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedToIntFunction<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedUnaryOperator<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
- CheckedUnsupportedOperationException - Exception in org.anchoranalysis.core.exception
-
When a particular operation is unsupported in particular circumstances.
- CheckedUnsupportedOperationException() - Constructor for exception CheckedUnsupportedOperationException
-
Creates with a default message indicating that the operation is unsupported.
- CheckedUnsupportedOperationException(String) - Constructor for exception CheckedUnsupportedOperationException
-
Creates with a message explaining that the operation is unsupported.
- CheckException - Exception in org.anchoranalysis.mpp.feature.error
-
- CheckException(String) - Constructor for exception CheckException
-
- CheckException(String, Throwable) - Constructor for exception CheckException
-
- CheckException(Throwable) - Constructor for exception CheckException
-
- checkExtentMatch(BoundingBox, BoundingBox) - Static method in class ExtentMatchHelper
-
Checks that the
Extents of two bounding boxes are identical.
- checkIdenticalDataType(VoxelDataType) - Method in class VoxelsUntyped
-
Do the voxels have a data-type that is equal to match?
- CheckIfAllowed - Class in org.anchoranalysis.io.output.writer
-
- CheckIfAllowed(SingleLevelOutputEnabled, Optional<WriterExecuteBeforeEveryOperation>, Writer) - Constructor for class CheckIfAllowed
-
- checkIfConnected() - Method in class ObjectMask
-
Determines if an object-mask is connected.
- CheckMark - Class in org.anchoranalysis.mpp.feature.bean.mark
-
A predicate on a mark to check if a condition has been satisfied.
- CheckMark() - Constructor for class CheckMark
-
- CheckMarkWithMask - Class in org.anchoranalysis.plugin.mpp.bean.check
-
- CheckMarkWithMask() - Constructor for class CheckMarkWithMask
-
- checkMisconfigured(BeanInstanceMap) - Method in class AnchorBean
-
Checks that a bean's properties conform to expectations.
- CheckMisconfigured - Class in org.anchoranalysis.bean.initializable
-
Routines for checking that particular patterns exist with bean-properties.
- checkMisconfigured(BeanInstanceMap) - Method in class SequenceInteger
-
- checkMisconfigured(BeanInstanceMap) - Method in class FeatureEvaluator
-
- checkMisconfigured(BeanInstanceMap) - Method in class OutputWriteSettings
-
- checkMisconfigured(BeanInstanceMap) - Method in interface FeedbackReceiver
-
- checkMisconfigured(BeanInstanceMap) - Method in class FromStack
-
- checkMisconfigured(BeanInstanceMap) - Method in class ExtractSliceRange
-
- checkMisconfigured(BeanInstanceMap) - Method in class Erode
-
- checkMisconfigured(BeanInstanceMap) - Method in class Sequence
-
- checkMisconfigured(BeanInstanceMap) - Method in class ThreeChannels
-
- checkMisconfigured(BeanInstanceMap) - Method in class ThreeColoredObjects
-
- checkMisconfigured(BeanInstanceMap) - Method in class FromChannelOrMask
-
- checkMisconfigured(BeanInstanceMap) - Method in class PermuteFeature
-
- checkMisconfigured(BeanInstanceMap) - Method in class PermuteFeatureSequenceInteger
-
- checkMisconfigured(BeanInstanceMap) - Method in class Intersection
-
- checkMisconfigured(BeanInstanceMap) - Method in class IntensityMeanShellBase
-
- checkMisconfigured(BeanInstanceMap) - Method in class LastDirectories
-
- checkMisconfigured(BeanInstanceMap) - Method in class CoupledManifestsInputManager
-
- checkMisconfigured(BeanInstanceMap) - Method in class HOGFeature
-
- checkMisconfigured(BeanInstanceMap) - Method in class FromDictionary
-
- checkMisconfigured(BeanInstanceMap) - Method in class QuickExperiment
-
- checkMisconfigured(BeanInstanceMap) - Method in class QuickMultiDatasetExperiment
-
- checkMisconfigured(BeanInstanceMap) - Method in class MultiInputManagerQuick
-
- checkMisconfigured(BeanInstanceMap) - Method in class NamedChannelsQuick
-
- checkMisconfigured(BeanInstanceMap) - Method in class ExperimentResultsExperimentStructure
-
- checkMisconfigured(BeanInstanceMap) - Method in class ExperimentStructure
-
- checkMisconfigured(BeanInstanceMap) - Method in class QuickMultiDatasetStructuredExperiment
-
- CheckParsedFilePathBag - Class in org.anchoranalysis.plugin.io.bean.file.group.check
-
- CheckParsedFilePathBag() - Constructor for class CheckParsedFilePathBag
-
- checkResultVector(ResultsVector) - Static method in class ConstantsInListFixture
-
checks that a result-vector has the results we expect from the feature-list associated with
this fixture
- checkSize(Extent) - Method in class HOGParameters
-
Throws an exception if an image of size extent cannot be described by these
parameters.
- checkUnsupported3D(Channel) - Static method in class SegmentChannelIntoObjects
-
- checkUnsupportedObjectMask(Optional<ObjectMask>) - Static method in class SegmentChannelIntoObjects
-
- checkUnsupportedSeeds(Optional<ObjectCollection>) - Static method in class SegmentChannelIntoObjects
-
- ChildCacheFinder - Interface in org.anchoranalysis.feature.session.cache.finder
-
Strategy to determine which child-cache (among hierarchy) to employ for a particular feature
calculation.
- childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in interface FeatureCalculationCache
-
Gets/creates a child-cache for a given name.
- childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in class CheckCacheForSpecificChildren
-
- childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in interface ChildCacheFinder
-
Selects a child-cache given a parent and a child-name.
- childCacheFor(FeatureCalculationCache<?>, CacheCreator, ChildCacheName, V) - Method in class DefaultChildCacheFinder
-
- ChildCacheName - Class in org.anchoranalysis.feature.calculate.cache
-
A unique identifier for a child-cache's name commposed potentially of two elements.
- ChildCacheName(Class<?>) - Constructor for class ChildCacheName
-
Uses only the class as an identifier.
- ChildCacheName(Class<?>, int) - Constructor for class ChildCacheName
-
Uses only the class combines with an integer part-name.
- ChildCacheName(Class<?>, String) - Constructor for class ChildCacheName
-
Uses both the class and a part-name as an identifier.
- children() - Method in class ErrorNodeImpl
-
- ChooseOneList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- ChooseOneList() - Constructor for class ChooseOneList
-
- Circle - Class in org.anchoranalysis.mpp.mark.conic
-
A circle
- Circle(Bound) - Constructor for class Circle
-
Creates with a radius within particular bounds.
- Circle(Circle) - Constructor for class Circle
-
Copy constructor
- Circle() - Constructor for class Circle
-
- circleAt(Point2i, double) - Static method in class CircleObjectFixture
-
- CircleObjectFixture - Class in org.anchoranalysis.test.feature.plugins.objects
-
- circumference(int) - Method in class Ellipse
-
- clamp(Point3i, Dimensions) - Static method in class PointClamper
-
- clamp(Point3d, Dimensions) - Static method in class PointClamper
-
- ClampHistogramMax - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Clamps the input-histogram to a certain maximum value, and then delegates the calculate-level.
- ClampHistogramMax() - Constructor for class ClampHistogramMax
-
- clampTo(Extent) - Method in class BoundingBox
-
Ensures that the box fits inside a
Extent by reducing any values to their limits in
the respective dimension.
- classificationString(boolean) - Static method in class BinaryOutcomeImageLabeller
-
- classInCurrentJar() - Method in class LauncherConfig
-
A class which we use to determine the base location for pathRelativeProperties.
- clean() - Method in class VoxelizedMarksWithEnergy
-
- clean() - Method in class EnergyMemoList
-
- cleanUp(VoxelPartitionFactory<T>) - Method in class IndexByChannel
-
- cleanUp(VoxelPartitionFactory<T>) - Method in class IndexByRegion
-
- cleanUp(VoxelPartitionFactory<T>) - Method in interface VoxelPartition
-
- cleanUp(VoxelPartitionFactory<Histogram>) - Method in class VoxelPartitionHistogram
-
- cleanUp() - Method in interface VoxelizedMark
-
- clear() - Method in class FeatureList
-
Removes all of the elements from this list.
- clear() - Method in class UnsignedBuffer
-
- clear() - Method in class UpdatableMarksList
-
- clearBest() - Method in class DualState
-
- clipTo(T, Extent) - Method in interface AccessObjectMask
-
Ensures the element lies within a certain extent.
- clipTo(ObjectMask, Extent) - Method in class AccessObjectMaskSimple
-
- clipTo(Extent) - Method in class ObjectMask
-
Makes sure an object fits inside an extent, removing any parts which do not.
- close() - Method in interface Progress
-
- close() - Method in class ProgressConsole
-
- close() - Method in class ProgressIgnore
-
- close() - Method in class ProgressIncrement
-
- close() - Method in class ProgressMultiple
-
- close(boolean, boolean) - Method in class StatefulNullMessageLogger
-
- close(boolean, boolean) - Method in class ConsoleMessageLogger
-
- close(boolean, boolean) - Method in class FailureOnlyMessageLogger
-
- close(boolean, boolean) - Method in class MessageLoggerList
-
- close(boolean, boolean) - Method in interface StatefulMessageLogger
-
- close(boolean, boolean) - Method in class TextFileMessageLogger
-
- close() - Method in class FeatureCSVWriter
-
Closes any open file-handles.
- close() - Method in interface OpenedImageFile
-
Closes the opened image-file, removing any intermediate data-structures.
- close() - Method in class CSVWriter
-
- close() - Method in class CSVReader.OpenedCSVFile
-
- close() - Method in class ReadByLine
-
Closes any opened-files
- close(ErrorReporter) - Method in interface InputFromManager
-
Performs all tidying up, file-closing etc.
- close(ErrorReporter) - Method in class InputFromManagerDelegate
-
- close(ErrorReporter) - Method in class MultiInput
-
- close(ErrorReporter) - Method in class StackWithMap
-
- close() - Method in class SharedStateFilteredImageOutput
-
- close() - Method in class SharedStateSelectedSlice
-
- close() - Method in class OpenedMultiFile
-
- close() - Method in class OnnxModel
-
- close() - Method in class OpenCVModel
-
- closeAndWriteOutputs(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, Function<InputOutputContext, FeatureCSVWriterCreator>, InputOutputContext) - Method in class FeatureExporter
-
Writes all the results that have been collected as a CSV file, and closes open I/O handles
and memory structures.
- closeAndWriteOutputs(ExportFeaturesStyle) - Method in class SharedStateSegmentInstance
-
Writes all the results that have been collected as a CSV file, and closes open I/O handles
and memory structures.
- closeAnyOpenIO() - Method in class FeatureResultsAndThumbnails
-
Closes any open IO and removes redundant structures stored in memory.
- closeLogger() - Method in class RecordingCounter
-
Closes the logger.
- ClusterByTimestamp - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster
-
Associates particular timestamp with each file, and clusters.
- ClusterByTimestamp() - Constructor for class ClusterByTimestamp
-
- clusterFor(File) - Method in class ClusterMembership
-
Finds the corresponding cluster for a particular file.
- ClusterIdentifier - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster
-
Uniquely identifies a cluster.
- ClusterIdentifier(ZoneOffset) - Constructor for class ClusterIdentifier
-
Creates with no name.
- ClusterIdentifier(String, ZoneOffset) - Constructor for class ClusterIdentifier
-
Creates with a constant-name.
- ClusterMembership - Class in org.anchoranalysis.plugin.io.file.copy
-
A mapping of files to membership of particular clusters.
- ClusterMembership(ClusterIdentifier) - Constructor for class ClusterMembership
-
- CODE_MINIMA - Static variable in class WatershedEncoding
-
- CODE_PLATEAU - Static variable in class WatershedEncoding
-
- CODE_TEMPORARY - Static variable in class WatershedEncoding
-
- CODE_UNVISITED - Static variable in class WatershedEncoding
-
- CoefficientOfVarianceFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- CoefficientOfVarianceFromAll() - Constructor for class CoefficientOfVarianceFromAll
-
- coefficientOfVariation(Histogram) - Static method in class HistogramStatistics
-
Calculates the coefficient-of-variation of a distribution of values, represented by
their histogram.
- CoefficientOfVariation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- CoefficientOfVariation() - Constructor for class CoefficientOfVariation
-
- CollapseFileName - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive
-
Removes the file-name from a path, but keeps the directories and preserves the file-extension.
- CollapseFileName() - Constructor for class CollapseFileName
-
- CollectionGenerator<T> - Class in org.anchoranalysis.io.generator.collection
-
Writes a collection of elements as a subdirectory with each element as a single file in the
subdirectory.
- CollectionGenerator(Generator<T>, String) - Constructor for class CollectionGenerator
-
- collectResult() - Method in interface ProcessChangedPointAbsoluteMasked
-
Collects the result of the operation after processing neighbor voxels.
- collectResult() - Method in interface ProcessVoxelNeighbor
-
Collects the result of the operation after processing neighbor pixels.
- collectResult() - Method in interface ProcessVoxelNeighborAbsolute
-
Collects the result of the operation after processing neighbor voxels.
- colorAxis(Axis) - Method in class PlotColorScheme
-
- colorChart(JFreeChart) - Method in class PlotColorScheme
-
- ColorConverterBase - Class in org.anchoranalysis.plugin.opencv.bean.color
-
Converts a RGB stack into another color space using OpenCV.
- ColorConverterBase() - Constructor for class ColorConverterBase
-
- ColoredBase - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Base class for providers that draw entities (an outline or filled) on a background
- ColoredBase() - Constructor for class ColoredBase
-
- ColoredBaseWithGenerator - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Like
ColoredBase but uses a generator to determine the colors for the objects
- ColoredBaseWithGenerator() - Constructor for class ColoredBaseWithGenerator
-
- ColoredMarks - Class in org.anchoranalysis.mpp.mark
-
- ColoredMarks() - Constructor for class ColoredMarks
-
- ColoredMarks(MarkCollection, ColorIndex, IdentifierGetter<Mark>) - Constructor for class ColoredMarks
-
- ColoredMarks(Mark, RGBColor) - Constructor for class ColoredMarks
-
- ColoredMarks(MarkCollection, ColorList) - Constructor for class ColoredMarks
-
- ColoredMarks - Class in org.anchoranalysis.plugin.mpp.bean.stack.provider
-
Draws a colored representation (outline or filled) of an
MarkCollection on a background
- ColoredMarks() - Constructor for class ColoredMarks
-
- ColoredMarksWithDisplayStack - Class in org.anchoranalysis.mpp.io.marks
-
- ColoredMarksWithDisplayStack(MarksWithDisplayStack, ColorIndex, IdentifierGetter<Mark>) - Constructor for class ColoredMarksWithDisplayStack
-
- ColoredMarksWithDisplayStack(ColoredMarks, DisplayStack) - Constructor for class ColoredMarksWithDisplayStack
-
- ColoredMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Draws a colored representation (outline or filled) of a
ObjectMask on a background
- ColoredMask() - Constructor for class ColoredMask
-
- ColoredObjectCollection - Class in org.anchoranalysis.plugin.image.object
-
- ColoredObjectCollection() - Constructor for class ColoredObjectCollection
-
Create with an empty collection.
- ColoredObjectCollection(ObjectMask, RGBColor) - Constructor for class ColoredObjectCollection
-
Create with a single object and color.
- ColoredObjectCollection(ObjectCollection, ColorList) - Constructor for class ColoredObjectCollection
-
Create with an existing object and color list.
- ColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Draws a colored representation (outline or filled) of an
ObjectCollection on a background
- ColoredObjects() - Constructor for class ColoredObjects
-
- coloredObjectsToDraw(Dimensions) - Method in class ColoredBase
-
Creates colored-objects to be drawn.
- coloredObjectsToDraw(Dimensions) - Method in class ColoredBaseWithGenerator
-
- coloredObjectsToDraw(Dimensions) - Method in class ColoredMask
-
- coloredObjectsToDraw(Dimensions) - Method in class ThreeColoredObjects
-
- ColoredOverlayCollection - Class in org.anchoranalysis.overlay.collection
-
- ColoredOverlayCollection() - Constructor for class ColoredOverlayCollection
-
- ColoredOverlayCollection(OverlayCollection, ColorList) - Constructor for class ColoredOverlayCollection
-
- colorFor(ObjectWithProperties, int) - Method in class ObjectDrawAttributes
-
A color for a particular object
- colorForEachIndex(int) - Method in class ColorScheme
-
Assigns a color to each index value from a list of size numberColors.
- ColorIndex - Interface in org.anchoranalysis.core.color
-
Associates an RGB-color with each index.
- ColorIndexModulo - Class in org.anchoranalysis.core.color
-
Derives a new
ColorIndex from an existing
ColorIndex applying a modulo operation
to each index call.
- ColorIndexModulo(ColorIndex) - Constructor for class ColorIndexModulo
-
- colorLegend(LegendTitle) - Method in class PlotColorScheme
-
- ColorList - Class in org.anchoranalysis.core.color
-
A list of colors, each corresponding to a particular index position.
- ColorList(Color...) - Constructor for class ColorList
-
Create for one or more colors of type
Color.
- ColorList(RGBColor...) - Constructor for class ColorList
-
Create for one or more colors of type
RGBColor.
- ColorList() - Constructor for class ColorList
-
- colorPlot(XYPlot) - Method in class PlotColorScheme
-
- colorPlot(CategoryPlot) - Method in class PlotColorScheme
-
- ColorProvider - Class in org.anchoranalysis.image.bean.provider
-
- ColorProvider() - Constructor for class ColorProvider
-
- ColorScheme - Class in org.anchoranalysis.bean.shared.color.scheme
-
Creates a sequence of related colors.
- ColorScheme() - Constructor for class ColorScheme
-
- ColorSchemeUnary - Class in org.anchoranalysis.bean.shared.color.scheme
-
- ColorSchemeUnary() - Constructor for class ColorSchemeUnary
-
- ColorSchemeUnary(ColorScheme) - Constructor for class ColorSchemeUnary
-
- colorSpaceCode() - Method in class ColorConverterBase
-
The color space conversion code to use from OpenCV, that defines the color-space to convert
to.
- colorSpaceCode() - Method in class ConvertRGBToHSV
-
- colorSpaceCode() - Method in class ConvertRGBToLab
-
- column(int) - Method in class RotationMatrix
-
Extracts a column from the rotation-matrix as a point.
- ColumnDefinition - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
-
- ColumnDefinition() - Constructor for class ColumnDefinition
-
- combine(List<PermutationAssigner>) - Static method in class PermutationAssignerFactory
-
- Combine - Class in org.anchoranalysis.image.io.bean.object.draw
-
- Combine() - Constructor for class Combine
-
- Combine(List<DrawObject>) - Constructor for class Combine
-
- combine(boolean, boolean) - Method in class MultiLevelAnd
-
- combine(boolean, boolean) - Method in class MultiLevelBinary
-
- combine(boolean, boolean) - Method in class MultiLevelOr
-
- combine(boolean, boolean) - Method in class SingleLevelAnd
-
- combine(boolean, boolean) - Method in class SingleLevelBinary
-
- combine(boolean, boolean) - Method in class SingleLevelOr
-
- Combine - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- Combine() - Constructor for class Combine
-
- CombineBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
- CombineBase() - Constructor for class CombineBase
-
- CombineCSV - Class in org.anchoranalysis.plugin.io.bean.task
-
Combines multiple CSV files into a single CSV file.
- CombineCSV() - Constructor for class CombineCSV
-
- combined() - Method in class PathDifference
-
The directory-component (if it exists) and filename-component combined.
- combined() - Method in class SplitPath
-
A path that combines the root together with the remainder.
- combineDescription(String, String) - Method in class AddConstantTo
-
- combineDescription(String, String) - Method in class ConstantToThePowerOf
-
- combineDescription(String, String) - Method in class DivideByConstant
-
- combineDescription(String, String) - Method in class MultiplyByConstant
-
- combineDescription(String, String) - Method in class SubtractFrom
-
- combineDescription(String, String) - Method in class ToThePowerOfConstant
-
- combineDescription(String, String) - Method in class ReplaceUnusualValue
-
- combineDescription(String, String) - Method in class WithValueBase
-
- combineDescriptionsRecursively(String, String) - Method in exception AnchorCombinableException
-
Traverses through a set of nested-exceptions creating a description for each "combined"
exception, and combining them into a single string.
- CombinedListGenerator<T> - Class in org.anchoranalysis.io.generator.combined
-
Several generators combined together with a common element-type.
- CombinedListGenerator(NameValue<Generator<T>>) - Constructor for class CombinedListGenerator
-
- CombinedListGenerator(Stream<NameValue<Generator<T>>>) - Constructor for class CombinedListGenerator
-
- CombinedListGenerator(Generator<T>...) - Constructor for class CombinedListGenerator
-
- CombinedListGenerator() - Constructor for class CombinedListGenerator
-
- CombinedName - Class in org.anchoranalysis.feature.io.name
-
A name which is unique when a primaryName is combined with a secondaryName
- CombinedName(String, String) - Constructor for class CombinedName
-
Creates with explicit strings for both parts.
- CombineObjectsForFeatures<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine
-
A way to combine (or not combine) objects so that they provide a feature-table.
- CombineObjectsForFeatures() - Constructor for class CombineObjectsForFeatures
-
- CombineRasterGenerator<T> - Class in org.anchoranalysis.image.io.bean.stack.combine
-
Combines a number of generators of Raster images by tiling their outputs together
- CombineRasterGenerator() - Constructor for class CombineRasterGenerator
-
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelAnd
-
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelBinary
-
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class MultiLevelOr
-
- CombineToOnePath - Class in org.anchoranalysis.plugin.mpp.contour.path.merge
-
- combineToOnePath(List<ContiguousVoxelPath>) - Static method in class CombineToOnePath
-
Combines all the contiguous paths to a single-path.
- CombineTypes - Class in org.anchoranalysis.image.voxel.datatype
-
Calculates which
VoxelDataType to use when combining two other voxel-data types, but
without losing precision.
- combineTypes(VoxelDataType, VoxelDataType) - Static method in class CombineTypes
-
What data-type to use to represent voxels of both type1 and type2?
- combineValueAndFeature(double, double) - Method in class AddConstantTo
-
- combineValueAndFeature(double, double) - Method in class ConstantToThePowerOf
-
- combineValueAndFeature(double, double) - Method in class DivideByConstant
-
- combineValueAndFeature(double, double) - Method in class MultiplyByConstant
-
- combineValueAndFeature(double, double) - Method in class SubtractFrom
-
- combineValueAndFeature(double, double) - Method in class ToThePowerOfConstant
-
- combineValueAndFeature(double, double) - Method in class ReplaceUnusualValue
-
- combineValueAndFeature(double, double) - Method in class WithValueBase
-
- combineWithSuffix(String) - Method in class FilenameSplitExtension
-
Inserts a suffix after the base-name, but before the extension, immutably.
- CommandLineException - Exception in org.anchoranalysis.launcher
-
An exception thrown at run-time while processing command-line args
- CommandLineException(String) - Constructor for exception CommandLineException
-
- CommandLineExtracter - Class in org.anchoranalysis.launcher.options
-
Adds methods to CommandLine for querying and extracting options, with and without
arguments.
- CommandLineExtracter(CommandLine) - Constructor for class CommandLineExtracter
-
- CommandLineOptions - Class in org.anchoranalysis.launcher.options
-
All command-line options used by the launcher.
- common() - Method in class InitializationContext
-
- common() - Method in interface InputOutputContext
-
Creates a
CommonContext a context that contains a subset of this context.
- CommonContext - Class in org.anchoranalysis.core.log
-
A logger with additional configuration that are coupled together widely in the code
- CommonContext(Logger, Path) - Constructor for class CommonContext
-
- CommonPath - Class in org.anchoranalysis.core.system.path
-
Finds the common root directory of a set of paths.
- commonType(Stream<VoxelDataType>) - Static method in class FindCommonVoxelType
-
Finds a common type to represent (ideally without loss of precision} of a stream of types.
- commonType(VoxelDataType, VoxelDataType) - Static method in class FindCommonVoxelType
-
Finds a common type to represent (ideally without loss of precision} both first and
second.
- ComparableSource - Class in org.anchoranalysis.annotation.io.bean.comparer
-
A set of elements, loaded from the file-system, to be compared to another set.
- ComparableSource() - Constructor for class ComparableSource
-
- Comparator3d<T extends Tuple3d> - Class in org.anchoranalysis.spatial.point
-
Imposes an ordering on any sub-type of
Tuple3d.
- Comparator3d() - Constructor for class Comparator3d
-
- Comparator3i<T extends Tuple3i> - Class in org.anchoranalysis.spatial.point
-
Imposes an ordering on any sub-type of
Tuple3i.
- Comparator3i() - Constructor for class Comparator3i
-
- ComparatorOrderByName<V> - Class in org.anchoranalysis.core.identifier.name
-
- ComparatorOrderByName() - Constructor for class ComparatorOrderByName
-
- compare(NameValue<V>, NameValue<V>) - Method in class ComparatorOrderByName
-
- compare(T, T) - Method in class Comparator3d
-
- compare(T, T) - Method in class Comparator3i
-
- CompareAnnotations<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
-
Task to compare a set of annotations to a segmentation or another set of annotations.
- CompareAnnotations() - Constructor for class CompareAnnotations
-
- compareTo(AssociatedIndex) - Method in class Indexable
-
- compareTo(MultiName) - Method in class CombinedName
-
- compareTo(MultiName) - Method in class SimpleName
-
- compareTo(EigenvalueAndVector) - Method in class EigenvalueAndVector
-
- compareTo(SortedSetChannel) - Method in class SortedSetChannel
-
- compareTo(SortedSetSlice) - Method in class SortedSetSlice
-
- compareTo(BoundingBox) - Method in class BoundingBox
-
- compareTo(Extent) - Method in class Extent
-
- compareTo(ReadableTuple3i) - Method in interface ReadableTuple3i
-
- CompareWithRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
Compares a value with a range, returning specified constants if its inside the range, below it or
above it
- CompareWithRange() - Constructor for class CompareWithRange
-
- CompareWithRangeFeature<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
- CompareWithRangeFeature() - Constructor for class CompareWithRangeFeature
-
- CompareXML - Class in org.anchoranalysis.test
-
Compares two XML documents to see if they are equal.
- comparison() - Method in interface ImageCounterWithStatistics
-
Creates statistics from counted images and the payload T passed for annotated images.
- ComparisonSharedState<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
-
- ComparisonSharedState(CSVAssignment, int, Function<String, ImageCounterWithStatistics<T>>) - Constructor for class ComparisonSharedState
-
- CompatibleWithMark - Interface in org.anchoranalysis.mpp.mark
-
- completeProjection() - Method in interface ProjectableBuffer
-
Performs any final operation before turning the projected buffer.
- Compose<S,T,U> - Class in org.anchoranalysis.mpp.segment.transformer
-
Combines a transformation from S to U with one from U to T
- Compose() - Constructor for class Compose
-
- Compose(StateTransformerBean<S, U>, StateTransformerBean<U, T>) - Constructor for class Compose
-
- CompressAnyTIFF - Class in org.anchoranalysis.plugin.io.bean.file.copy.method
-
Create a voxelwise
compressed copy of any TIFF file being copied, and otherwise do a
Bytewise copy.
- CompressAnyTIFF() - Constructor for class CompressAnyTIFF
-
- computeIfAbsent(K) - Method in class MapCreate
-
Gets an existing element from the map, newly creating and storing the element if it's absent.
- computeInitialFeasibleSolution() - Method in class HungarianAlgorithm
-
Compute an initial feasible solution by assigning zero labels to the workers and by assigning
to each job a label equal to the minimum cost among its incident edges.
- Concatenate - Class in org.anchoranalysis.bean.define.adder
-
Concatenates a list of adders.
- Concatenate() - Constructor for class Concatenate
-
- Concatenate - Class in org.anchoranalysis.plugin.image.bean.color.provider
-
- Concatenate() - Constructor for class Concatenate
-
- Concatenate - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
- Concatenate() - Constructor for class Concatenate
-
- Concatenate - Class in org.anchoranalysis.plugin.image.bean.stack.provider
-
Combines all the channels from one or more sources (stacks, channels etc.)
- Concatenate() - Constructor for class Concatenate
-
- Concatenate<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Concatenates the inputs from multiple
InputManagers that all provide the same input-type.
- Concatenate() - Constructor for class Concatenate
-
- ConcatenateFileTypes - Class in org.anchoranalysis.io.generator
-
Concatenates the arrays of
FileType that may be returned from write operations.
- ConcatenateFileTypes() - Constructor for class ConcatenateFileTypes
-
Creates to always use a list for tracking.
- ConcatenateFileTypes(boolean) - Constructor for class ConcatenateFileTypes
-
- ConcurrentJobMonitor - Class in org.anchoranalysis.experiment.task.processor
-
- ConcurrentJobMonitor(long) - Constructor for class ConcurrentJobMonitor
-
- ConditionalKernel - Class in org.anchoranalysis.image.voxel.kernel
-
Executes another
BinaryKernel iff a predicate is satisfied for a particular point.
- ConditionalKernel(BinaryKernel, Predicate<Point3i>) - Constructor for class ConditionalKernel
-
Creates with a particular delegate
BinaryKernel and a predicate that tests each
point.
- ConfigureBioformatsLogging - Class in org.anchoranalysis.io.bioformats
-
Singleton class for making sure Bioformats is configured configured.
- configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteDivideByParam
-
- configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFeatureSequenceInteger
-
- configurePermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFirstSecondOrder
-
- ConicBase - Class in org.anchoranalysis.mpp.mark.conic
-
- ConicBase() - Constructor for class ConicBase
-
- ConicBase(MarkWithPosition) - Constructor for class ConicBase
-
- ConicFitterBase - Class in org.anchoranalysis.plugin.points.bean.fitter
-
- ConicFitterBase() - Constructor for class ConicFitterBase
-
- ConnectedComponentsFromBinarySegmentation - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Performs a binary-segmentation of the channel and converts its connected-components into objects
- ConnectedComponentsFromBinarySegmentation() - Constructor for class ConnectedComponentsFromBinarySegmentation
-
- ConnectedComponentsFromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
-
Converts a binary-mask into its connected components
- ConnectedComponentsFromMask() - Constructor for class ConnectedComponentsFromMask
-
- considerVisit(Point3i, int, ObjectMask) - Method in class VisitScheduler
-
- considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerAnd
-
- considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerConvexAboutRoot
-
- considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerMaxDistanceAlongContour
-
- considerVisit(Point3i, int, ObjectMask) - Method in class VisitSchedulerUniformSample
-
- ConsiderVisit - Interface in org.anchoranalysis.plugin.mpp.contour
-
Whether to visit a point or not.
- ConsistentChannelChecker - Class in org.anchoranalysis.plugin.image.task.grouped
-
Checks that the histograms created from channels all have the same data type, res, max-value etc.
- ConsistentChannelChecker() - Constructor for class ConsistentChannelChecker
-
- ConsoleAccepted - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- ConsoleAccepted() - Constructor for class ConsoleAccepted
-
- ConsoleAggregatedReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- ConsoleAggregatedReporter(double) - Constructor for class ConsoleAggregatedReporter
-
- ConsoleAggregatedReporter() - Constructor for class ConsoleAggregatedReporter
-
- ConsoleMessageLogger - Class in org.anchoranalysis.experiment.log
-
- ConsoleMessageLogger() - Constructor for class ConsoleMessageLogger
-
- Constant<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
-
A constant value that is entirely invariant to the feature-input.
- Constant(double) - Constructor for class Constant
-
Constructor with a particular value.
- Constant(String, double) - Constructor for class Constant
-
Constructor with a particular value and a custom-name.
- Constant() - Constructor for class Constant
-
- Constant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
A constant value for thresholding.
- Constant() - Constructor for class Constant
-
- Constant(int) - Constructor for class Constant
-
- Constant - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Always generates a constant path irrespective of the the input
- Constant() - Constructor for class Constant
-
- Constant(String) - Constructor for class Constant
-
- Constant - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
- Constant() - Constructor for class Constant
-
- ConstantScaleFactor - Class in org.anchoranalysis.plugin.image.bean.scale
-
- ConstantScaleFactor() - Constructor for class ConstantScaleFactor
-
- ConstantsInListFixture - Class in org.anchoranalysis.test.feature
-
- ConstantToThePowerOf<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- ConstantToThePowerOf() - Constructor for class ConstantToThePowerOf
-
- ConstantWeight - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
-
All marks have weight of 1
- ConstantWeight() - Constructor for class ConstantWeight
-
- consumeChannelIfSupported(int, BiConsumer<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>>, Consumer<Channel>) - Method in class ChannelMapper
-
- containerOptional() - Method in class WithContainerBase
-
- containerRequired() - Method in class WithContainerBase
-
- contains(Double) - Method in class DoubleList
-
- contains(Double) - Method in class DoubleSet
-
- contains(Integer) - Method in class IntegerList
-
- contains(Integer) - Method in class IntegerSet
-
- contains(T) - Method in interface PrimitiveBeanCollection
-
Whether the collection contains a particular element?
- contains(String) - Method in class StringList
-
- contains(String) - Method in class StringSet
-
- contains(ChildCacheName) - Method in class CacheTransferSourceCollection
-
- contains(Feature<FeatureInput>) - Method in class SharedFeatures
-
Whether a particular feature is contained in this instance.
- contains(Point3d) - Method in class Dimensions
-
Is a point of type
Point3d contained within the extent?
- contains(Point3i) - Method in class Dimensions
-
- contains(BoundingBox) - Method in class Dimensions
-
Is box entirely contained within the extent?
- contains(Point3i) - Method in class IntersectingObjects
-
All elements that contain a particular point.
- contains(Point3i) - Method in class ObjectMask
-
Whether a particular point exists within the object-mask?
- contains(double) - Method in class ResolvedBound
-
- contains(Object) - Method in class UpdatableMarksList
-
- contains(Object) - Method in class MarkCollection
-
- contains() - Method in class BoundingBox
-
For evaluating whether this bounding-box contains other points, boxes etc.?
- contains(Point2i) - Method in class Extent
-
Is a point of type
Point2i contained within the extent in the XY plane?
- contains(Point3d) - Method in class Extent
-
Is a point of type
Point3d contained within the extent?
- contains(ReadableTuple3i) - Method in class Extent
-
- contains(int, int, int) - Method in class Extent
-
Is a point contained within the extent?
- contains(BoundingBox) - Method in class Extent
-
Is box entirely contained within the extent?
- contains(ReadableTuple3i) - Method in class BoundingBoxRTree
-
Which objects contain a particular point?
- contains(double) - Method in class IntervalRTree
-
Which objects contain a particular point?
- containsAll(Collection<?>) - Method in class UpdatableMarksList
-
- containsChild(ChildCacheName) - Method in class CacheTransferSource
-
- containsEdge(V, V) - Method in class GraphWithoutPayload
-
Does the graph contain a particular edge?
- containsEdge(V, V) - Method in class GraphWithPayload
-
Does the graph contain a particular edge?
- containsFamily(Class<?>) - Method in class BeanInstanceMap
-
Is a particular family-type contained in the map?
- containsKey(String) - Method in class Dictionary
-
Does a parameter exist with a particular key?
- containsMark(Mark) - Method in class RandomCollectionWithAddCriteria
-
- containsOrEmpty() - Method in class DebugModeParameters
-
- containsStream(ReadableTuple3i) - Method in class BoundingBoxRTree
-
- containsStream(double) - Method in class IntervalRTree
-
- containsStream(Point) - Method in class RTree
-
Which objects contain a particular point?
- containsVertex(V) - Method in class GraphWithoutPayload
-
Does the graph contain a particular vertex?
- containsVertex(V) - Method in class GraphWithPayload
-
Does the graph contain a particular vertex?
- containsX(double) - Method in class Extent
-
Is a value contained within the extent on the X-axis?
- containsX(int) - Method in class Extent
-
Is a value contained within the extent on the X-axis?
- containsY(double) - Method in class Extent
-
Is a value contained within the extent on the Y-axis?
- containsY(int) - Method in class Extent
-
Is a value contained within the extent on the Y-axis?
- containsZ(double) - Method in class Extent
-
Is a value contained within the extent on the Z-axis?
- containsZ(int) - Method in class Extent
-
Is a value contained within the extent on the Z-axis?
- ContiguousVoxelPath - Class in org.anchoranalysis.plugin.mpp.contour.path
-
A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
- ContiguousVoxelPath(Point3i, Point3i) - Constructor for class ContiguousVoxelPath
-
With a single initial-point, and maybe a connection point
- ContiguousVoxelPath() - Constructor for class ContiguousVoxelPath
-
Without any connection-point
- continueFurther(int, double, int, MessageLogger) - Method in class TerminationCondition
-
Whether to continue for an additional iteration step or not.
- continueFurther(int, double, int, MessageLogger) - Method in class TerminationConditionListOr
-
- continueFurther(int, double, int, MessageLogger) - Method in class TriggerTerminationCondition
-
- continueFurther(int, double, int, MessageLogger) - Method in class NumberIterations
-
- continueFurther(int, double, int, MessageLogger) - Method in class UnchangedBase
-
- Contour - Class in org.anchoranalysis.spatial.point
-
A path of successively-neighbored points.
- Contour() - Constructor for class Contour
-
- contoursForObject(ObjectMask) - Static method in class CVFindContours
-
- ContourTraverser - Class in org.anchoranalysis.plugin.mpp.contour
-
Iteratively moves around a
ObjectMask that describes the contour of an object.
- ContourTraverser(ObjectMask, ConsiderVisit, boolean, boolean) - Constructor for class ContourTraverser
-
- ConversionPolicy - Enum in org.anchoranalysis.image.core.channel.convert
-
The different ways of converting the voxel-data-type in a
Channel.
- convert(Channel, ConversionPolicy) - Method in class MaxIntensity
-
- convert(Channel, ConversionPolicy) - Method in interface ChannelConverterAttached
-
Converts the voxel-type in a
Channel.
- convert(Channel, ConversionPolicy) - Method in class MaxIntensityFromHistogram
-
- convert(Channel, ConversionPolicy) - Method in class QuantileIntensityFromHistogram
-
- convert(Channel, ConversionPolicy) - Method in class UpperLowerQuantileIntensityFromHistogram
-
- convert(Stack, ConversionPolicy) - Method in class ChannelConverter
-
- convert(Channel, ConversionPolicy) - Method in class ChannelConverter
-
Converts channel to have voxels with data-type T.
- convert(Channel, VoxelDataType) - Method in class ChannelConverterMulti
-
Converts a
Channel's voxels to another type.
- convert(DisplayStack) - Static method in class ConvertDisplayStackToRGB
-
- convert(ByteBuffer, int, OrientationChange, boolean) - Method in class ConvertTo
-
- convert(ByteBuffer, int, OrientationChange, boolean) - Method in class UnsignedByteFromUnsignedByte
-
- convert(Mark) - Method in class MarkToObjectConverter
-
- Convert<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
Converts a channel by applying a converter (no histogram is involved in the conversion).
- Convert() - Constructor for class Convert
-
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class ChannelConvertStyle
-
Converts a particular set of channels.
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class IndependentChannels
-
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class RGB
-
- convert(int) - Method in class NumberToStringConverter
-
Converts number to a string, padding with leading zeros if necessary to ensure the
desired width.
- convert2iTo3d(List<Point2i>) - Static method in class PointConverter
-
- convert2iTo3f(List<Point2i>) - Static method in class PointConverter
-
- convert3dTo3f(List<Point3d>) - Static method in class PointConverter
-
- convert3fTo3d(List<Point3f>) - Static method in class PointConverter
-
- convert3i(List<Point3f>, boolean) - Static method in class PointConverter
-
Convert a list of
Point3f to a list of
Point3i, optionally rounding values.
- convert3i(List<Point3d>) - Static method in class PointConverter
-
- convert3iTo3f(List<Point3i>) - Static method in class PointConverter
-
- ConvertBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
- ConvertBase() - Constructor for class ConvertBase
-
- convertBeforeAssign(DisplayStack) - Method in class DisplayStackGenerator
-
- convertBeforeAssign(Stack) - Method in class FlattenStackGenerator
-
- convertBeforeAssign(T) - Method in class RasterGeneratorBridge
-
- convertBeforeAssign(T) - Method in class RasterGeneratorDelegateToRaster
-
Converts an element before setting it on the delegate.
- convertBeforeTransform(Stack) - Method in class DisplayStackGenerator
-
- convertBeforeTransform(Stack) - Method in class FlattenStackGenerator
-
- convertBeforeTransform(Stack) - Method in class RasterGeneratorBridge
-
- convertBeforeTransform(Stack) - Method in class RasterGeneratorDelegateToRaster
-
- ConvertChannelTo<T> - Class in org.anchoranalysis.image.bean.channel.converter
-
Converts a channel from one type to another.
- ConvertChannelTo() - Constructor for class ConvertChannelTo
-
- ConvertChannelToWithHistogram<T> - Class in org.anchoranalysis.image.bean.channel.converter
-
Creates a
ChannelConverterAttached<Histogram, T> for converting a channel to a particular
type, making use of a
Histogram.
- ConvertChannelToWithHistogram() - Constructor for class ConvertChannelToWithHistogram
-
- convertCode(int, int, EncodedVoxels, Point3i) - Method in class EncodedIntBuffer
-
Convert code to connected-component
- convertCropped(DisplayStack, BoundingBox) - Static method in class ConvertDisplayStackToRGB
-
- ConvertDisplayStackToRGB - Class in org.anchoranalysis.image.io.stack
-
- ConvertedInput<U extends InputFromManager> - Class in org.anchoranalysis.plugin.mpp.experiment.shared
-
A converted-input, together with any logged messages associated with it.
- ConvertedInput(U, StringBuilder) - Constructor for class ConvertedInput
-
- ConvertedToRuntimeException(Throwable) - Constructor for exception CheckedStream.ConvertedToRuntimeException
-
Creates for any exception.
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteNoScaling
-
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMaxValue
-
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMinMaxValue
-
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByType
-
- convertFloat(FloatBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
-
- convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType
-
- convertFloat(FloatBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
FloatBuffer to the current position in
a buffer of type
T.
- convertFrom(VoxelsUntyped, VoxelsFactoryTypeBound<T>) - Method in class VoxelsConverter
-
Creates a new voxels of type T and copies the voxels from from.
- ConvertFromImagePlus - Class in org.anchoranalysis.io.imagej.convert
-
Converts an ImagePlus into a channel or voxels.
- ConvertFromMat - Class in org.anchoranalysis.plugin.opencv.convert
-
Convert from the OpenCV
Mat to a
Stack.
- ConvertFromPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
converts a feature to a physical distance in a XY place that is isometric
- ConvertFromPhysicalVolume() - Constructor for class ConvertFromPhysicalVolume
-
- convertFromUnits(double, String) - Static method in class SpatialUnits
-
Converts a value from another unit-type to base units.
- convertFromUnits(double, SpatialUnits.UnitSuffix) - Static method in class SpatialUnits
-
Converts a value from another unit-type to base units.
- ConvertImageFormat - Class in org.anchoranalysis.plugin.image.task.bean.format
-
Converts each input-image to an output format, optionally changing the bit depth.
- ConvertImageFormat() - Constructor for class ConvertImageFormat
-
- ConvertNamedChannels<T extends NamedChannelsInput,S,U extends InputFromManager> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.convert
-
- ConvertNamedChannels() - Constructor for class ConvertNamedChannels
-
- ConvertNamedChannelsInputToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
- ConvertNamedChannelsInputToStack(NamedChannelsInput) - Constructor for class ConvertNamedChannelsInputToStack
-
Create with an input.
- ConvertNamedChannelsInputToStack(NamedChannelsInput, int, Optional<String>) - Constructor for class ConvertNamedChannelsInputToStack
-
Create with an input.
- ConvertNamedChannelsToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
- ConvertNamedChannelsToStack() - Constructor for class ConvertNamedChannelsToStack
-
- ConvertRGBToHSV - Class in org.anchoranalysis.plugin.opencv.bean.color
-
- ConvertRGBToHSV() - Constructor for class ConvertRGBToHSV
-
- ConvertRGBToLab - Class in org.anchoranalysis.plugin.opencv.bean.color
-
- ConvertRGBToLab() - Constructor for class ConvertRGBToLab
-
- convertSliceOfSingleChannel(ByteBuffer, int, OrientationChange) - Method in class ConvertTo
-
Converts a slice of single-channel into a newly created
VoxelBuffer.
- ConvertTo<T> - Class in org.anchoranalysis.io.bioformats.copyconvert
-
Converts a subset of raw voxel bytes in a buffer to a possibly a buffer with different data-type.
- ConvertTo(Function<VoxelsUntyped, Voxels<T>>, IntFunction<T>, Function<T, VoxelBuffer<T>>) - Constructor for class ConvertTo
-
- convertTo3d(Point2d) - Static method in class PointConverter
-
Convert a
Point2d to a
Point3d using
0 as the value of the Z-axis
component.
- convertTo3i(Point2i) - Static method in class PointConverter
-
Convert a
Point2i to a
Point3i using
0 as the value of the Z-axis
component.
- convertTo3i(Point2i, int) - Static method in class PointConverter
-
Convert a
Point3i to a
Point2i using an explicit value for the Z-axis
component.
- ConvertToFactory - Class in org.anchoranalysis.io.bioformats.copyconvert
-
- ConvertToImagePlus - Class in org.anchoranalysis.io.imagej.convert
-
Converts a channel or voxels into a ImagePlus.
- ConvertToImageProcessor - Class in org.anchoranalysis.io.imagej.convert
-
Converts other voxel data-structures (as used by Anchor) to an ImageJ ImageProcessor.
- ConvertToImg - Class in org.anchoranalysis.image.voxel.convert.imglib2
-
- ConvertToMat - Class in org.anchoranalysis.plugin.opencv.convert
-
Converts common image data-structures used by Anchor to the Mat class used by OpenCV.
- ConvertToNativeImg - Class in org.anchoranalysis.image.voxel.convert.imglib2
-
- convertToObjects(Dimensions) - Method in interface AnnotationWithMarks
-
Creates an object-collection that is a voxelized representation of the marks in the
annotation.
- convertToOutputType(Channel) - Method in class GradientBase
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertFromPhysicalVolume
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalAreaXY
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalDistance
-
- convertToPhysical(double, UnitConverter) - Method in class ConvertToPhysicalVolume
-
- convertToPhysical(double, UnitConverter) - Method in class FeatureConvertUnits
-
- ConvertToPhysicalAreaXY<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
- ConvertToPhysicalAreaXY() - Constructor for class ConvertToPhysicalAreaXY
-
- ConvertToPhysicalDistance<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
- ConvertToPhysicalDistance(Feature<T>, SpatialUnits.UnitSuffix, DirectionVector) - Constructor for class ConvertToPhysicalDistance
-
- ConvertToPhysicalDistance() - Constructor for class ConvertToPhysicalDistance
-
- ConvertToPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
-
converts a feature to a physical distance in a XY place that is isometric
- ConvertToPhysicalVolume() - Constructor for class ConvertToPhysicalVolume
-
- convertToString(Path) - Static method in class PathOperations
-
Converts a path to a string, making sure it uses UNIX-style separators.
- convertToUnits(double, String) - Static method in class SpatialUnits
-
Converts a value in base-units to another unit-type.
- convertToUnits(double, SpatialUnits.UnitSuffix) - Static method in class SpatialUnits
-
Converts a value in base-units to another unit-type.
- ConvertToVoxelBuffer - Class in org.anchoranalysis.io.imagej.convert
-
Converts a ImageProcessor to a voxel-buffer of particular data-type.
- ConvertUnits<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.physical
-
- ConvertUnits() - Constructor for class ConvertUnits
-
- convertUnsignedByte(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class ToByte
-
- convertUnsignedByte(UnsignedByteBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
-
- convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType
-
- convertUnsignedByte(UnsignedByteBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
UnsignedByteBuffer to the current
position in a buffer of type
T.
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteNoScaling
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMaxValue
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMinMaxValue
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByType
-
- convertUnsignedInt(UnsignedIntBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
-
- convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType
-
- convertUnsignedInt(UnsignedIntBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
UnsignedIntBuffer to the current
position in a buffer of type
T.
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteNoScaling
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMaxValue
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByMinMaxValue
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class ToByteScaleByType
-
- convertUnsignedShort(UnsignedShortBuffer, FloatBuffer) - Method in class ToFloatNoScaling
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class ToShortNoScaling
-
- convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class ToShortScaleByType
-
- convertUnsignedShort(UnsignedShortBuffer, T) - Method in class VoxelsConverter
-
Copies a value from the current position in a
UnsignedShortBuffer to the current
position in a buffer of type
T.
- convertValue(short) - Method in class ToUnsignedShort
-
- convertValue(short) - Method in class UnsignedShortFromSignedShort
-
- convertValue(short) - Method in class UnsignedShortFromUnsignedShort
-
- ConvertWithHistogram<T> - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
Converts a channel to a different voxel data-type by applying a converter with an associated
histogram.
- ConvertWithHistogram() - Constructor for class ConvertWithHistogram
-
- ConvexHull2D - Class in org.anchoranalysis.plugin.points.bean.convexhull
-
Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
- ConvexHull2D() - Constructor for class ConvexHull2D
-
- convexHull2D(List<Point2i>) - Static method in class ConvexHullUtilities
-
- convexHull2D(List<Point2i>, int) - Static method in class ConvexHullUtilities
-
Apply a convex-hull algorithm to filter a set of points.
- ConvexHull3D - Class in org.anchoranalysis.plugin.points.bean.convexhull
-
- ConvexHull3D() - Constructor for class ConvexHull3D
-
- ConvexHullBase - Class in org.anchoranalysis.plugin.points.bean.convexhull
-
- ConvexHullBase() - Constructor for class ConvexHullBase
-
- ConvexHullUtilities - Class in org.anchoranalysis.plugin.points.convexhull
-
- copyAllChannels(Dimensions, ByteBuffer, DestinationChannelForIndex, int, ImageFileEncoding, OrientationChange) - Method in class ConvertTo
-
- copyAllFrames(IFormatReader, List<Channel>, Progress, ImageFileShape, ConvertTo<?>, ReadOptions, OrientationChange) - Static method in class CopyConvert
-
Copies all frames, channels, z-slices (in a byte-array) into a destination set of
Channels converting them if necessary along the way.
- copyChange(MarkCollection) - Method in class MarksFromPartition
-
Makes a copy, with different marks
- copyChangeDictionary(Dictionary) - Method in class EnergyStack
-
- copyChangeIterationsDilation(int) - Method in class MorphologicalIterations
-
Copies the bean setting an new value for iterationsDilation
- copyChangeOrientation(ByteBuffer, boolean, int, T, OrientationChange) - Method in class ConvertTo
-
Copy the bytes, changing orientation.
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class ToUnsignedByteWithScaling
-
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class UnsignedByteFromFloat
-
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class UnsignedByteFromUnsignedByteInterleaving
-
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer, OrientationChange) - Method in class UnsignedByteFromUnsignedByteNoInterleaving
-
- copyChangeOrientation(ByteBuffer, boolean, int, FloatBuffer, OrientationChange) - Method in class FloatFromUnsignedByte
-
- copyChangeOrientation(ByteBuffer, boolean, int, FloatBuffer, OrientationChange) - Method in class FloatFromUnsignedInt
-
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedIntBuffer, OrientationChange) - Method in class UnsignedIntFromUnsignedInt
-
- copyChangeOrientation(ByteBuffer, boolean, int, UnsignedShortBuffer, OrientationChange) - Method in class ToUnsignedShort
-
- CopyContext<T> - Class in org.anchoranalysis.plugin.io.input.path
-
Context parameters when copying many files from a source directory to a destination directory.
- CopyContext(Path, Path, T) - Constructor for class CopyContext
-
- CopyConvert - Class in org.anchoranalysis.io.bioformats.copyconvert
-
Copies the bytes from a IFormatReader to a list of channels, converting if necessary.
- CopyFiles<T> - Class in org.anchoranalysis.plugin.io.bean.task
-
Copy files to the output-directory, possibly changing the name or performing other operations
like compression in the process.
- CopyFiles() - Constructor for class CopyFiles
-
- CopyFilesMethod - Class in org.anchoranalysis.plugin.io.bean.file.copy.method
-
A method used for copying files (e.g.
- CopyFilesMethod() - Constructor for class CopyFilesMethod
-
- CopyFilesNaming<T> - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
How an output name (and path) is selected for an input file when copying.
- CopyFilesNaming() - Constructor for class CopyFilesNaming
-
- CopyFilesNamingOne - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
- CopyFilesNamingOne() - Constructor for class CopyFilesNamingOne
-
- CopyFilesNamingWithoutSharedState - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Base class for implementations of
CopyFilesNaming where each file is copied independently
of the others.
- CopyFilesNamingWithoutSharedState() - Constructor for class CopyFilesNamingWithoutSharedState
-
- copyFrom(int, int, ResultsVector, int) - Method in class ResultsVector
-
Copies a contiguous subset of results from another vector.
- copyFrom(VoxelsUntyped, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source (of any type) to voxels of type T.
- copyFromFloat(Voxels<FloatBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link FloatBuffer} to voxels of type T.
- copyFromUnsignedByte(Voxels<UnsignedByteBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type T.
- copyFromUnsignedInt(Voxels<UnsignedIntBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type T.
- copyFromUnsignedShort(Voxels<UnsignedShortBuffer>, Voxels<T>) - Method in class VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type T.
- copyInit(Class<?>, NamedProviderStore<S>) - Method in class PopulateStoreFromDefine
-
Copies objects of a particular class from the define AND initializes
- copyKeepOrientation(ByteBuffer, boolean, int, T) - Method in class ConvertTo
-
Copy the bytes, without changing orientation.
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class ToUnsignedByteWithScaling
-
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class UnsignedByteFromFloat
-
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class UnsignedByteFromUnsignedByteInterleaving
-
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedByteBuffer) - Method in class UnsignedByteFromUnsignedByteNoInterleaving
-
- copyKeepOrientation(ByteBuffer, boolean, int, FloatBuffer) - Method in class FloatFromUnsignedByte
-
- copyKeepOrientation(ByteBuffer, boolean, int, FloatBuffer) - Method in class FloatFromUnsignedInt
-
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedIntBuffer) - Method in class UnsignedIntFromUnsignedInt
-
- copyKeepOrientation(ByteBuffer, boolean, int, UnsignedShortBuffer) - Method in class ToUnsignedShort
-
- copyObjectsFrom(NamedProvider<ObjectCollection>) - Method in class ImageInitialization
-
- copyPixelsTo(int, BoundingBox, Voxels<UnsignedByteBuffer>, BoundingBox) - Method in class DisplayStack
-
Copies pixels from a particular channel to an output buffer.
- copyProvider(Class<?>, NamedProviderStore<T>) - Method in class PopulateStoreFromDefine
-
Copies objects of a particular class from the define AND initializes as a provider
- copyStacksFrom(NamedProvider<Stack>) - Method in class ImageInitialization
-
- copyTo(SharedObjects, Logger) - Method in interface ExportSharedObjects
-
Adds any exported shared-objects to sharedObjects.
- copyTo(SharedObjects, Logger) - Method in class MultiInput
-
- copyTo(SharedObjects, Logger) - Method in class FromCSVInput
-
- copyToDirectory(File) - Method in class TestLoader
-
Copies all the data in the test-data folder (recursively), preserving file modification
times.
- copyToDirectory(String[], File) - Method in class TestLoader
-
Copies specific subdirectories from the test-data folder (recursively), preserving file
modification times.
- copyVoxelFrom(int, VoxelBuffer<T>, int) - Method in class VoxelBuffer
-
Copies one particular intensity-value from another
VoxelBuffer into this buffer.
- copyVoxelsTo(BoundingBox, VoxelsUntyped, BoundingBox) - Method in class VoxelsUntyped
-
Copies the voxels into a destination, but only those voxels inside a bounding-box.
- copyVoxelsTo(ObjectMask, VoxelsUntyped, BoundingBox) - Method in class VoxelsUntyped
-
Copies the voxels into a
destination, but only those voxels inside an
ObjectMask.
- copyWithoutInit(Class<?>, NamedProviderStore<S>) - Method in class PopulateStoreFromDefine
-
Copies objects of a particular class from the define WITHOUT doing any initialization
- cornerMin() - Method in class BoundedVoxels
-
The minimum corner of the bounding box in each dimension.
- cornerMin() - Method in class BoundingBox
-
The minimum corner of the bounding box in each dimension.
- correctedEndIndex(int) - Method in class IndexRangeNegative
-
The end-index, maybe corrected so that it is no longer negative.
- correctedStartIndex(int) - Method in class IndexRangeNegative
-
The start-index, maybe corrected so that it is no longer negative.
- CostMatrix<T> - Class in org.anchoranalysis.annotation.io.assignment
-
Stores costs between all possible pairings between elements from two lists.
- CostOverlapWithinMidpointDistance - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
TODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheable
- CostOverlapWithinMidpointDistance() - Constructor for class CostOverlapWithinMidpointDistance
-
- Count - Class in org.anchoranalysis.feature.bean.results
-
The number of the results from a particular feature.
- Count() - Constructor for class Count
-
- count() - Method in class PredicateAtCorner
-
- count() - Method in class PredicateImplementation
-
- count() - Method in interface VoxelsPredicate
-
Counts the number of values satisfying the predicate - across all voxels.
- count(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>) - Method in class CountIntersectingVoxels
-
- Count - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
Counts the number of items in a histogram (posssibly in relation to a threshold: above, below
etc.)
- Count() - Constructor for class Count
-
- countByte(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class CountVoxelsIntersectingBounded
-
Counts all voxels in the intersection of two bounded-voxels of type
BoundedVoxels
that match a predicate.
- countByteMasked(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class CountVoxelsIntersectingBounded
-
Counts all voxels intersection of two bounded-voxels of type
BoundedVoxels but only
voxels that lie on an object-mask and match a predicate.
- CountEqual - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
-
- CountEqual() - Constructor for class CountEqual
-
- Counter - Class in org.anchoranalysis.math.arithmetic
-
A simple counter that increments.
- Counter() - Constructor for class Counter
-
- countForObject(ObjectMask) - Method in class PredicateAtCorner
-
- countForObject(ObjectMask) - Method in class PredicateImplementation
-
- countForObject(ObjectMask) - Method in interface VoxelsPredicate
-
Counts the number of values satisfying the predicate - but restricted to voxels corresponding
to on in an object-mask.
- countIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class CountVoxelsIntersectingObjects
-
Counts the number of intersecting-voxels between two object-masks.
- countIntersectingVoxels(ObjectMask) - Method in class ObjectMask
-
Counts the number of intersecting-voxels between two object-masks.
- CountIntersectingVoxels - Class in org.anchoranalysis.mpp.overlap
-
Counts the number of intersecting-pixels where bytes are encoded as region memberships
- CountIntersectingVoxels(byte) - Constructor for class CountIntersectingVoxels
-
- CountIntersectingVoxels(PredicateRegionMembership) - Constructor for class CountIntersectingVoxels
-
- countIntersectingVoxels() - Method in class MaxIntensityProjectionPair
-
- CountKernel - Class in org.anchoranalysis.image.voxel.kernel.count
-
Base class for kernels that return a count (positive integer) for every voxel.
- CountKernel() - Constructor for class CountKernel
-
Creates with a kernel-size of three.
- CountKernelNeighborhood - Class in org.anchoranalysis.image.voxel.kernel.count
-
For every voxel on the outline, count all neighbors that are adjacent.
- CountKernelNeighborhood() - Constructor for class CountKernelNeighborhood
-
- CountKernelNeighborhoodMask - Class in org.anchoranalysis.image.voxel.kernel.count
-
The number of touching-faces of a voxel with a neighbor, so long as the neighbor is part of an
ObjectMask.
- CountKernelNeighborhoodMask(ObjectMask) - Constructor for class CountKernelNeighborhoodMask
-
Create with object-mask.
- countMasked(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, byte) - Method in class CountIntersectingVoxels
-
- countMatching(IntPredicate) - Method in class Histogram
-
Gets the total count of all values that match a predicate.
- countOff() - Method in class BinaryVoxels
-
Counts the number of voxels with an off state.
- countOn() - Method in class BinaryVoxels
-
Counts the number of voxels with an on state.
- countThreshold(RelationToThreshold) - Method in interface VoxelStatistics
-
Counts the number of voxels that exist, relative to a threshold.
- countThreshold(RelationToThreshold) - Method in class VoxelStatisticsCombined
-
- countThreshold(RelationToThreshold) - Method in class VoxelStatisticsFromHistogram
-
- CountVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
- CountVoxelsIntersectingObjects - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
- countXY() - Method in class RunningSumPoint
-
The count for the X or Y dimensions.
- countZ() - Method in class RunningSumPoint
-
The count for the Z dimension.
- CoupledManifests - Class in org.anchoranalysis.plugin.io.manifest
-
- CoupledManifests(DeserializedManifest, int, Logger) - Constructor for class CoupledManifests
-
- CoupledManifests(Manifest, DeserializedManifest, Logger) - Constructor for class CoupledManifests
-
- CoupledManifestsInputManager - Class in org.anchoranalysis.plugin.io.bean.input.manifest
-
- CoupledManifestsInputManager() - Constructor for class CoupledManifestsInputManager
-
- create(List<T>, List<T>, boolean, CheckedToDoubleBiFunction<T, T, CreateException>) - Static method in class CostMatrix
-
Creates by calculating the cost between elements.
- create(Provider<T>) - Static method in class OptionalProviderFactory
-
Creates from a provider if non-null.
- create() - Method in class RandomNumberGeneratorBean
-
- create() - Method in class EqualToBean
-
- create() - Method in class GreaterThanBean
-
- create() - Method in class GreaterThanEqualToBean
-
- create() - Method in class LessThanBean
-
- create() - Method in class LessThanEqualToBean
-
- create() - Method in class RelationBean
-
- create() - Method in class StringMap
-
Derives a
Map representation for the mapping.
- create(boolean, T) - Static method in class OptionalFactory
-
Creates only if a boolean flag is true, otherwise returns Optional.empty().
- create(boolean, Supplier<T>) - Static method in class OptionalFactory
-
Creates only if a boolean flag is true, otherwise returns Optional.empty().
- create(String) - Static method in class OptionalFactory
-
Creates Optional.empty() for an empty string, or otherwise Optional.of().
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class LoggingDestination
-
Creates a logger for this destination
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class OnlyIf
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class SwitchDetailedLogging
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToConsole
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToMultiple
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToTextFile
-
- create(OutputterChecked, ErrorReporter, ExecutionArguments, boolean) - Method in class ToTextFileOnlyIfFailure
-
- create(boolean) - Static method in class ExecutionTimeRecorderFactory
-
Creates either a
ExecutionTimeRecorder that records times, or ignores the recording
depending on whether any output is enabled that needs the execution-time.
- create(Class<? extends FeatureInput>) - Method in interface CacheCreator
-
- create(SharedObjects) - Static method in class FeatureRelatedInitialization
-
Creates with shared-objects, and otherwise empty initialization.
- create(Logger, Path) - Static method in class FeatureRelatedInitialization
-
Creates a log and a model-directory, and otherwise empty initialization.
- create(FeatureCSVMetadata, Outputter, boolean) - Static method in class FeatureCSVWriter
-
- create(Optional<String>, String) - Static method in class MultiNameFactory
-
Creates either a multi-name that is either has a single part or a double part.
- create(FeatureOutputMetadata, FeatureCSVWriterCreator, boolean) - Static method in class FeatureCalculationResultsFactory
-
Creates with appropriate support classes for outputting.
- create(FeatureCSVMetadata) - Method in interface FeatureCSVWriterCreator
-
- create(Class<? extends FeatureInput>) - Method in class HorizontalCacheCreator
-
- create() - Method in class ImgLib2Lanczos
-
- create() - Method in class ImgLib2Linear
-
- create() - Method in class InterpolatorBean
-
- create() - Method in class None
-
- create(Stack) - Static method in class BufferedImageFromStack
-
- create(Dimensions, VoxelDataType) - Method in class ChannelFactory
-
Creates an empty initialized channel for a particular data-type.
- create(Voxels<?>) - Method in class ChannelFactory
-
Create a
Channel from particular voxels.
- create(Voxels<?>, Optional<Resolution>) - Method in class ChannelFactory
-
Create a
Channel from particular voxels.
- create(Voxels<?>, Optional<Resolution>) - Method in class ChannelFactorySingleType
-
Create a
Channel from voxels and a resolution.
- create(String) - Static method in class ImageSizeSuggestionFactory
-
Creates a suggestion for how to resize an image.
- create(Map<Integer, T>, UnaryOperator<T>) - Method in class DecodeLabels
-
Creates a map of elements to other elements that are labelled with unique integers
(sequentially increasing) in voxels.
- create(int) - Method in class DecodeLabels
-
Creates a list of elements from voxels that are labelled with unique integers (sequentially
increasing).
- create(Collection<Point3i>) - Static method in class ObjectFromPointsFactory
-
- create(Channel) - Static method in class DisplayStack
-
- create(Stack) - Static method in class DisplayStack
-
- create(RGBStack) - Static method in class DisplayStack
-
- create(Optional<SharedObjects>, Optional<EnergyStack>) - Static method in class InitializationFactory
-
- create(InputOutputContext) - Static method in class ImageInitializationFactory
-
- create(InputOutputContext, Optional<ImageSizeSuggestion>) - Static method in class ImageInitializationFactory
-
- create() - Static method in class RasterDirectoryObjectsGenerator
-
- create(SliceBufferIndex<T>) - Method in interface VoxelsFactoryTypeBound
-
- create(ObjectCollection, Extent, boolean, boolean) - Static method in class NeighborGraph
-
Create the graph with object-masks as vertices, where edges represent the number of
neighboring voxels between objects.
- create(List<V>, Function<V, ObjectMask>, Extent, boolean, boolean) - Static method in class NeighborGraph
-
- create(ObjectCollection) - Static method in class IntersectingObjects
-
- create(IFormatReader, VoxelDataType, int) - Static method in class ConvertToFactory
-
- create(Path) - Static method in class CSVWriter
-
Creates and starts a CSVWriter (it's always allowed, so will never return null)
- create(String, Optional<ManifestDescription>, OutputterChecked, String) - Static method in class TextFileOutputter
-
- create() - Method in class InterpolatorBeanImageJ
-
- create(InputManagerParameters) - Method in class FilesProvider
-
Creates or provides a list of files.
- create(InputManagerParameters) - Method in class FilesProviderUnary
-
- create(InputManagerParameters) - Method in class FilesProviderWithDirectory
-
- create(InputManagerParameters) - Method in class SpecificPathList
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class AddToDefaults
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class IgnoreUnderscorePrefixUnless
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class NoneExcept
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class OutputEnabledRules
-
Creates rules for determining whether an output is enabled or disabled.
- create(Optional<MultiLevelOutputEnabled>) - Method in class Permissive
-
- create(Optional<MultiLevelOutputEnabled>) - Method in class PermissiveExcept
-
- create(CommandLine, Path, Path) - Static method in class ExperimentExecutorFactory
-
Creates an experiment-executor from a command line that EITHER: uses a default-experiment OR
accepts a path passed as the first command-line argument
- create() - Method in class MarkEllipseFactory
-
- create() - Method in class MarkEllipsoidFactory
-
- create() - Method in class MarkFactory
-
- create() - Method in class MarkPointListFactory
-
- create() - Method in class EnergySchemeCreator
-
- create() - Method in class EnergySchemeCreatorByElement
-
- create(EnergyStackWithoutParameters) - Method in class DictionaryForImageCreator
-
- create(int) - Method in interface VoxelPartitionFactory
-
- create(int) - Method in class VoxelPartitonFactoryHistogram
-
- create(ImageInitialization, SharedObjects) - Static method in class PointsInitialization
-
- create(Optional<? extends ExportSharedObjects>, InitializationContext, Optional<Define>) - Static method in class MarksInitializationFactory
-
- create(List<Point3d>) - Static method in class PointListFactory
-
- create(List<Point3d>, int) - Static method in class PointListFactory
-
- create(IntToFloatFunction, Point2i) - Static method in class RotatableBoundingBoxFactory
-
Builds a bounding-box from the 5-element floating-point vector returned from the EAST
algorithm.
- create(Mark, EnergyStackWithoutParameters, RegionMap) - Static method in class PxlMarkMemoFactory
-
- create(Mark, EnergyStackWithoutParameters, RegionMap) - Static method in class VoxelizedMarkFactory
-
- create(Mark) - Method in class ProposerContext
-
- create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class Plot
-
Creates a graph
- create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class LinePlot
-
- create(InputManagerParameters) - Method in class FromAnnotations
-
- create() - Method in interface PermuteFirstSecondOrder.CreateFirstSecondOrder
-
- create(List<NamedBean<FeatureListProvider<T>>>, LabelHeaders, FeatureOutputNames, FeatureExporterContext) - Static method in class FeatureExporter
-
Alternative static constructor that creates a shared-state from a list of named
FeatureListProviders.
- create(NamedFeatureStore<T>, LabelHeaders, FeatureOutputNames, FeatureExporterContext) - Static method in class FeatureExporter
-
- create(FeatureOutputNames, FeatureTableCalculator<T>, LabelHeaders, FeatureExporterContext) - Static method in class FeatureExporter
-
- create(InputManagerParameters) - Method in class Combine
-
- create(InputManagerParameters) - Method in class Rooted
-
- create() - Method in class InterpolatorBeanOpenCV
-
- create(InputManagerParameters) - Method in class ExperimentResultsExperimentStructure
-
- create() - Static method in class ConstantsInListFixture
-
creates a feature-list associated with the fixture
- createAddCriteria() - Method in class EnergySchemeWithSharedFeatures
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class ReduceFirstAndSecond
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class ReduceRatioFirstAndSecond
-
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class SubtractReducedFromMerged
-
- createAndConsumeListBeans(String, HierarchicalConfiguration, Object, Collection<T>) - Static method in class BeanListCreator
-
Extracts a list of instantiated bean objects from an XML configuration, and adds them to
addTo.
- createAndStartSession() - Method in class ReportFeatureEvaluator
-
- createArguments(CommandLine) - Method in class LauncherConfig
-
- createAscending() - Static method in class HistogramFixture
-
a histogram from 0 to 255 (inclusive) where each bin is equal to its index (value 5 has count
5, value 100 has count 100 etc.)
- createAssignment(ObjectCollection, ObjectCollection, double, Dimensions) - Method in class AssignOverlappingObjects
-
Creates an assignment from the objects in left to those in right.
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class AnnotationComparisonAssigner
-
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class FeatureCostAssigner
-
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class MaskIntersectionAssigner
-
- createAxisArray() - Method in class GradientBaseAddSum
-
- createAxisArray() - Method in class GradientForAxis
-
- createAxisArray() - Method in class GradientXY
-
- createBackground(NamedProviderStore<Stack>, String) - Static method in class BackgroundCreator
-
- createBean(Class, BeanDeclaration, Object) - Method in class DefineFactory
-
- createBean(Class<?>, BeanDeclaration, Object) - Method in class AnchorDefaultBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class IncludeBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class IncludeListBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class ListBeanFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class DoubleListFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class DoubleSetFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class IntegerListFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class IntegerSetFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class StringListFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class StringSetFactory
-
- createBean(Class, BeanDeclaration, Object) - Method in class ReplacePropertyBeanFactory
-
- createBeanFromConfig(HierarchicalConfiguration, Object) - Static method in class BeanCreator
-
Creates a bean from a HierarchicalConfiguration.
- createBeanFromXML(XMLBeanDeclaration, String, Object) - Static method in class BeanCreator
-
Creates a bean from XML.
- createBetweenTwoPoints(Point3d, Point3d) - Static method in class DirectionVector
-
- createBetweenTwoPoints(Point3i, Point3i) - Static method in class DirectionVector
-
- createBounded(BoundingBox) - Method in interface VoxelsFactoryTypeBound
-
Creates and initializes voxels that correspond to a particular bounding-box region.
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in interface ArrangeStack
-
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class Overlay
-
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class Single
-
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class Tile
-
- createBufferedImage(int, int) - Method in class PlotInstance
-
- createBuilderWithDefaultErrorHandler() - Static method in class XMLParser
-
Creates a document-builder with default error-handling.
- createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class DerivedObject
-
- createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class Erode
-
- createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject>) - Method in class Shell
-
- createCalculationContext(Optional<String>, ExecutionTimeRecorder, InputOutputContext) - Method in class FeatureExporter
-
- createCalculationContext(ExecutionTimeRecorder, InputOutputContext) - Method in class SharedStateSegmentInstance
-
- createCalculator(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputStack, ? extends ReplaceStrategy<FeatureInputStack>>) - Method in class MergedPairsFeatures
-
- createChannel(int, boolean) - Method in class DisplayStack
-
Create
Channel for a particular
index after applying conversion.
- createChannel() - Method in class CheckMarkWithMask
-
- createChannelsForSeries(int, Progress, Logger) - Method in class NamedChannelsInput
-
- createChart(DefaultCategoryDataset, String, Optional<AxisLimits>) - Method in class BarPlot
-
Creates a chart
- createChart(DefaultBoxAndWhiskerCategoryDataset, String, Optional<AxisLimits>) - Method in class BoxPlot
-
- createChart(XYDataset, String, Optional<AxisLimits>) - Method in class LinePlot
-
Creates a chart
- createChart(S, String, Optional<AxisLimits>) - Method in class PlotIndexBase
-
- createChecked(boolean, CheckedSupplier<T, E>) - Static method in class OptionalFactory
-
- createCollection(Channel, ObjectCollection, CalculateLevel, int, MessageLogger) - Static method in class LevelResultCollectionFactory
-
- createColor(ColoredMarks, RegionMembershipWithFlags) - Static method in class OverlayCollectionMarkFactory
-
- createColors(int) - Method in class AssignmentColorPool
-
Creates a list of colors to describe the assignment.
- CreateCombinedStack - Class in org.anchoranalysis.image.bean.nonbean.init
-
- createComparisonStacks(AnnotationWithMarks, DisplayStack, Path, ColorScheme, Path, Logger, boolean) - Method in class MultipleComparer
-
Creates a
Stack illustrating the comparison between
annotation and each
source in
sources.
- createContextForWriting(Optional<ImageFileFormat>, ExecutionTimeRecorder) - Method in class OutputManager
-
- createConverter() - Method in class ConvertChannelTo
-
- createConverter() - Method in class ConvertChannelToWithHistogram
-
- createConverter() - Method in class ScaleByDictionary
-
- createConverter() - Method in class ScaleByMinMaxValue
-
- createConverter() - Method in class ScaleByTypeToByte
-
- createConverter() - Method in class ToByte
-
- createConverter() - Method in class ToByteUpperLowerQuantileIntensity
-
- createCountKernelMask(ObjectMask) - Method in class TouchingVoxels
-
- createDataset(Iterator<T>) - Method in class LinePlot
-
- createDataset(Iterator<T>) - Method in class PlotIndexBase
-
- createDataset(Iterator<T>) - Method in class PlotIndexBaseCategorical
-
Creates a sample dataset
- createDefaultDataset() - Method in class BarPlot
-
- createDefaultDataset() - Method in class BoxPlot
-
- createDefaultDataset() - Method in class PlotIndexBaseCategorical
-
- createDelegate(Feature<T>) - Method in class PermuteDivideByParam
-
- createDelegate(Feature<T>) - Method in class PermuteFeatureSequenceInteger
-
- createDelegate(Feature<T>) - Method in class PermuteFirstSecondOrder
-
- createDescending() - Static method in class HistogramFixture
-
- createDescriptor(Extent) - Method in class HOGParameters
-
Creates an empty
HOGDescriptor to describe an image of a particular size.
- createDesignMatrix(List<Point3f>) - Method in class LinearLeastSquaresViaNormalEquationBase
-
- createDictionary() - Method in class EnergyScheme
-
returns the associated
Dictionary or an empty set, if no dictionary is associated with the energy-scheme.
- createDim() - Method in class PointsFitterToMark
-
- createDimensions() - Method in class WithDimensionsBase
-
- createDims() - Method in class WithOptionalDimensionsBase
-
Returns the dimensions or null if none are provided
- createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>, float) - Method in class DistanceTransform3D
-
- createDuplicatePxlMarkMemoList() - Method in class VoxelizedMarksWithEnergy
-
- CreateEllipse - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
-
- CreateEllipse() - Constructor for class CreateEllipse
-
- createEmpty(Extent, VoxelDataType) - Method in class VoxelsFactory
-
Creates empty voxels to match a particular size.
- createEmptyInitialised(Dimensions) - Method in class ChannelFactorySingleType
-
Create a
Channel initialized with zero-valued voxel-buffers.
- createEmptyInitialisedToSupportMaxValue(Dimensions, long) - Method in class ChannelFactory
-
Creates an empty initialized channel with discrete type with as minimal as needed data-type
to support a maximum value.
- createEmptyMat(Extent, int) - Static method in class ConvertToMat
-
Creates a Mat which contains only zero-values.
- createEmptyOff(Extent) - Static method in class BinaryVoxelsFactory
-
Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off
(0).
- createEmptyOff(Extent, VoxelDataType) - Static method in class BinaryVoxelsFactory
-
Creates an empty binary-voxels of a particular data-type with all voxels initialized to
off.
- createEmptyOn(Extent) - Static method in class BinaryVoxelsFactory
-
Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to on
(255).
- createEmptyStackFor(Dimensions) - Static method in class ObjectsAsRGBGenerator
-
- createEmptyUninitialised(Dimensions) - Method in class ChannelFactorySingleType
-
Create a
Channel without initialization with voxel-buffers.
- CreateException - Exception in org.anchoranalysis.core.exception
-
A generic exception that be thrown when the creation of a new object fails.
- CreateException(String) - Constructor for exception CreateException
-
Creates with a message, but without a cause.
- CreateException(Throwable) - Constructor for exception CreateException
-
Creates with a cause, but without a message.
- CreateException(String, HasFriendlyErrorMessage) - Constructor for exception CreateException
-
Creates with a message, and a cause with a user-friendly error message.
- CreateException(String, AnchorCombinableException) - Constructor for exception CreateException
-
Creates with a message, and a combinable-exception as a cause.
- createExperimentExecutor(CommandLine) - Method in class LauncherConfig
-
- createExperimentOutputter(Optional<String>, Manifest, MultiLevelOutputEnabled, Optional<MultiLevelRecordedOutputs>, OutputWriteContext, PathPrefixerContext, Optional<Logger>) - Method in class OutputManager
-
Creates an outputter for the experiment in general.
- createExperimentState() - Method in class SegmentIntoMarks
-
- createExperimentState() - Method in class SegmentWithMarkedPointProcess
-
- createExporter(LabelHeaders, List<NamedBean<FeatureListProvider<U>>>, FeatureOutputNames, FeatureExporterContext) - Method in class FeatureSource
-
Creates the
FeatureExporter to be used for calculating and exporting feature-results.
- createExporter(LabelHeaders, List<NamedBean<FeatureListProvider<S>>>, FeatureOutputNames, FeatureExporterContext) - Method in class SingleRowPerInput
-
- createExporter(LabelHeaders, List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, FeatureOutputNames, FeatureExporterContext) - Method in class FromObjects
-
- CreateFeatureInput<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session
-
- createFeatureInput(Mark, RegionMap, EnergyStack) - Method in class FeatureValueCheckMark
-
- createFeatureInput(Mark, RegionMap, EnergyStack) - Method in class FeatureValueIndividualEnergyGreaterThan
-
- createFeatureInput(Mark, RegionMap, EnergyStack) - Method in class FeatureValueMarkGreaterEqualThan
-
- createFeatureList(String, TestLoader) - Static method in class FeaturesFromXmlFixture
-
- createFeatureNames() - Method in interface FeatureTableCalculator
-
Creates A list of names for each feature (columns of the table)
- createFeatureNames() - Method in class PairsTableCalculator
-
- createFeatureNames() - Method in class SingleTableCalculator
-
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class CombineObjectsForFeatures
-
Creates features that will be applied on the objects.
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class EachObjectIndependently
-
- createFeatures(NamedFeatureStore<FeatureInputSingleObject>) - Method in class EachObjectIndependently
-
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class PairNeighbors
-
- createFeatureSession() - Method in class FeatureEvaluator
-
Creates session for evaluating feature optionally adding an energy-stack.
- createFeatureSession(UnaryOperator<FeatureList<T>>, SharedObjects) - Method in class FeatureListEvaluator
-
Creates session for evaluating features.
- createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class AlwaysAllowed
-
- createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class CheckIfAllowed
-
- createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in interface Writer
-
The path to write a particular output to.
- createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class WriterRouterErrors
-
The path to write a particular output to.
- createFileOutputFor(String, FeedbackBeginParameters<VoxelizedMarksWithEnergy>, String) - Static method in class CSVReporterUtilities
-
- createFitResultFromMatrixAandCenter(DoubleMatrix2D, DoubleMatrix2D, boolean) - Static method in class EllipsoidFitHelper
-
- createFlat(boolean, Supplier<Optional<T>>) - Static method in class OptionalFactory
-
Creates an
Optional from a boolean flag and a supplier that returns an
Optional.
- createFloat(Extent, IntFunction<FloatBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createFloat(Voxels<FloatBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createFloat(Extent) - Static method in class MaxIntensityProjection
-
Creates a buffer for a max-intensity projection for float voxels.
- createFloat(Extent) - Static method in class MeanIntensityProjection
-
Creates a buffer for a mean-intensity projection for float voxels.
- createFloat(Voxels<FloatBuffer>) - Static method in class VoxelsExtracterFactory
-
- createForDirectoryPermissive(Path, boolean, Optional<Logger>) - Static method in class OutputterChecked
-
Creates, defaulting to a permissive output-manager in a particular directory.
- createForFeature(Feature<?>) - Method in interface CreateFeatureInput
-
- createForSingle(AnchorBean<?>, String) - Static method in class PermutationAssignerFactory
-
Creates an assigner for one or more properties, as identified by propertyPath.
- createForSubdirectory(String) - Method in class TestLoader
-
Creates a new test-loader for a subdirectory of the current test.
- createForVoxelBuffer(VoxelBuffer<T>, Extent) - Method in interface VoxelsFactoryTypeBound
-
Create a new
Voxels that has been
initialized with a single-slice's memory
buffers.
- createFrom(BufferedImage) - Static method in class CreateStackFromBufferedImage
-
- createFrom(Mask, int, boolean, boolean) - Static method in class FindContour
-
Creates an contour from a
Mask at the boundary of depth
1 pixel.
- createFrom(ObjectMask, int, boolean, boolean) - Static method in class FindContour
-
- createFrom(VoxelsUntyped, Optional<ObjectMask>) - Static method in class HistogramFromObjectsFactory
-
Creates a
Histogram of voxel intensity values in
voxels, all or only those in
object.
- createFrom(Channel, ObjectMask) - Static method in class HistogramFromObjectsFactory
-
Creates a
Histogram of voxel intensity values in
channel corresponding to
object.
- createFrom(Channel, ObjectCollection) - Static method in class HistogramFromObjectsFactory
-
Creates a
Histogram of voxel intensity values in
channel corresponding to
objects.
- createFrom(Channel, Mask) - Static method in class HistogramFromObjectsFactory
-
Creates a
Histogram of
all voxel intensity values in
channel
corresponding to
Mask.
- createFrom(int, ObjectMask) - Method in interface DecodeLabels.CreateElementFromScaledObject
-
Create from an index and it's scaled-object.
- createFrom(int, ObjectMask) - Method in interface AccessObjectMask
-
Creates an element of type T from an object-representation and index.
- createFrom(int, ObjectMask) - Method in class AccessObjectMaskSimple
-
- createFrom(SliceBufferIndex<T>, VoxelDataType) - Method in class VoxelsFactory
-
- createFrom(VoxelBuffer<?>) - Static method in class HistogramFactory
-
- createFrom(VoxelsUntyped) - Static method in class HistogramFactory
-
- createFromChannel(Channel) - Method in class ChannelProviderUnary
-
- createFromChannel(Channel) - Method in class AnisotropicDiffusion
-
- createFromChannel(Channel) - Method in class MinimumFilter
-
- createFromChannel(Channel) - Method in class Invert
-
- createFromChannel(Channel) - Method in class AssignFromDictionary
-
- createFromChannel(Channel) - Method in class AssignFromIntersectingObjects
-
- createFromChannel(Channel) - Method in class Convert
-
- createFromChannel(Channel) - Method in class ConvertWithHistogram
-
- createFromChannel(Channel) - Method in class Duplicate
-
- createFromChannel(Channel) - Method in class GradientBaseAddSum
-
- createFromChannel(Channel) - Method in class Sobel
-
- createFromChannel(Channel) - Method in class IfParamEquals
-
- createFromChannel(Channel) - Method in class Blur
-
- createFromChannel(Channel) - Method in class IfVoxelZero
-
- createFromChannel(Channel) - Method in class Median
-
- createFromChannel(Channel, ObjectCollection) - Method in class NormalizeDifferenceToMedian
-
- createFromChannel(Channel, ObjectCollection) - Method in class NormalizeObjectIntensity
-
- createFromChannel(Channel) - Method in class QuantileStretch
-
- createFromChannel(Channel) - Method in class ScaleXY
-
- createFromChannel(Channel) - Method in class UnaryWithMaskBase
-
- createFromChannel(Channel) - Method in class LevelPerObjectBase
-
- createFromChannel(Channel, ObjectCollection) - Method in class IdentifyObjects
-
- createFromChannel(Channel, ObjectCollection) - Method in class ScoreObjects
-
- createFromChannel(Channel) - Method in class ExtractCenterSlice
-
- createFromChannel(Channel) - Method in class ExtractSliceRange
-
- createFromChannel(Channel) - Method in class MaximumIntensityProjection
-
- createFromChannel(Channel) - Method in class MeanIntensityProjection
-
- createFromChannel(Channel) - Method in class UnaryWithObjectsBase
-
- createFromChannel(Channel, ObjectCollection) - Method in class UnaryWithObjectsBase
-
- createFromChannel(Channel) - Method in class UnaryWithValueBase
-
- createFromChannel(Channel) - Method in class SegmentChannel
-
- createFromChannel(Channel) - Method in class SegmentWithSeeds
-
- createFromChannel(Channel) - Method in class WithChannelBase
-
- createFromChannel(Channel, int) - Method in class BackgroundSubtractor
-
- createFromChannel(Channel) - Method in class EdgeFilterIJ
-
- createFromChannel(Channel) - Method in class GaussianBlur2D
-
- createFromChannel(Channel) - Method in class MedianFilter3D
-
- createFromChannel(Channel, int) - Method in class WithFilterBase
-
- createFromChannel(Channel) - Method in class WithRadiusBase
-
- createFromChannel(Channel, int) - Method in class WithRadiusBase
-
- createFromChannelWithConstant(Channel, double) - Method in class ArithmeticWithConstantBase
-
- createFromChannelWithConstant(Channel, double) - Method in class ArithmeticWithConstantConditionallyWriteBase
-
- createFromChannelWithConstant(Channel, double) - Method in class UnaryWithValueBase
-
- createFromDimensions(Dimensions) - Method in class DistanceTransformForEachObject3D
-
- createFromDimensions(Dimensions) - Method in class CreateNew
-
- createFromDimensions(Dimensions) - Method in class FromDimensionsBase
-
- createFromDimensions(Dimensions) - Method in class RepeatSlice
-
- createFromDimensions(Dimensions) - Method in class AllValuesOff
-
- createFromDimensions(Dimensions) - Method in class AllValuesOn
-
- createFromDimensions(Dimensions) - Method in class FromObjects
-
- createFromDimensions(Dimensions) - Method in class FromDimensionsBase
-
- createFromDimensions(Dimensions) - Method in class Box
-
- createFromExisting(InitializationContext, Optional<Define>, Optional<SharedObjects>, Optional<Dictionary>) - Static method in class MarksInitializationFactory
-
- createFromExplicitDirectory(String) - Static method in class TestLoader
-
Creates a new test-data loader using an explicit file path as root.
- createFromExplicitDirectory(Path) - Static method in class TestLoader
-
Creates a new test-data loader using an explicit file path as root.
- createFromFile(Path) - Method in class DeriveElementsFromSequencedDirectory
-
Creates an element of type T from a one particular file in the sequence.
- createFromFile(Path) - Method in class SequencedDirectoryDeserializer
-
- createFromGenerator(TransformingGenerator<BoundingBox, Stack>, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates an extracted-object generator that draws an outline - with default color green and
flattened in Z.
- createFromGuess3D(Mask, int, boolean, boolean) - Static method in class FindContour
-
- createFromHistogram(Histogram) - Method in class HistogramProviderUnary
-
- createFromHistogram(Histogram) - Method in class CutBelowThreshold
-
- createFromHistogram(Histogram) - Method in class GreaterThanThreshold
-
- createFromList(List<T>, Function<T, BoundingBox>) - Static method in class BoundedList
-
Creates for a list, minimally fitting a bounding-box around all elements
- createFromMarks(MarkCollection, KernelCalculationContext, Logger) - Static method in class VoxelizedMarksWithEnergyFactory
-
- createFromMask(Mask) - Method in class MaskProviderUnary
-
- createFromMask(Mask) - Method in class DistanceTransform3D
-
- createFromMask(Mask) - Method in class FromMask
-
- createFromMask(Mask) - Method in class FromMaskBase
-
- createFromMask(Mask) - Method in class CombineBase
-
- createFromMask(Mask) - Method in class Duplicate
-
- createFromMask(Mask) - Method in class Invert
-
- createFromMask(Mask) - Method in class ExteriorContour
-
- createFromMask(Mask) - Method in class FitBoxToOnVoxels
-
- createFromMask(Mask) - Method in class MorphologicalOperatorBase
-
- createFromMask(Mask) - Method in class IfPredicateBase
-
- createFromMask(Mask) - Method in class ScaleXY
-
- createFromMask(Mask) - Method in class FlattenZ
-
- createFromMask(Mask) - Method in class RepeatSlice
-
- createFromMask(Mask) - Method in class FillHoles
-
- createFromMask(Mask) - Method in class MorphologicalOperation
-
- createFromMask(Mask, Mask) - Method in class ConvexHull2D
-
- createFromMask(Mask, Mask) - Method in class ConvexHull3D
-
- createFromMask(Mask) - Method in class ConvexHullBase
-
- createFromMask(Mask, Mask) - Method in class ConvexHullBase
-
- createFromMaskedChannel(Channel, Mask) - Method in class SubtractMean
-
- createFromMaskedChannel(Channel, Mask) - Method in class AssignFromChannel
-
- createFromMaskedChannel(Channel, Mask) - Method in class AssignValue
-
- createFromMaskedChannel(Channel, Mask) - Method in class UnaryWithMaskBase
-
- createFromMaskedChannel(Channel, Mask) - Method in class ZeroOutsideMask
-
- createFromMavenWorkingDirectory() - Static method in class TestLoader
-
Creates a new test-data loader finding PATH_RESOURCES using the Maven working
directory.
- createFromMavenWorkingDirectory(String) - Static method in class TestLoader
-
Creates a new test-data loader finding PATH_RESOURCES/PLUS_SOMETHING using the Maven
working directory.
- createFromNotObjects(ObjectCollection, Dimensions, BinaryValuesInt) - Static method in class MaskFromObjects
-
- createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderUnary
-
- createFromObjects(ObjectCollection, Dimensions, BinaryValuesInt) - Static method in class MaskFromObjects
-
- createFromObjects(ObjectCollection) - Method in class AtIndex
-
- createFromObjects(ObjectCollection) - Method in class DecomposeIntoConnectedComponents
-
- createFromObjects(ObjectCollection) - Method in class RejectIfNotConnected
-
- createFromObjects(ObjectCollection) - Method in class Duplicate
-
- createFromObjects(ObjectCollection) - Method in class ObjectWithMaximumFeature
-
- createFromObjects(ObjectCollection) - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- createFromObjects(ObjectCollection) - Method in class SortByFeature
-
- createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class Filter
-
- createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class FilterByGroup
-
- createFromObjects(ObjectCollection) - Method in class IntersectsWithContainer
-
- createFromObjects(ObjectCollection) - Method in class Match
-
- createFromObjects(ObjectCollection) - Method in class NotInContainer
-
- createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderFilterBase
-
- createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class ObjectCollectionProviderFilterBase
-
- createFromObjects(ObjectCollection) - Method in class RemoveTouchingBorder
-
- createFromObjects(ObjectCollection) - Method in class AndObjectsWithMasks
-
- createFromObjects(ObjectCollection) - Method in class MergeGreedyToIncreaseObjectFeature
-
- createFromObjects(ObjectCollection) - Method in class MergeWithFeature
-
- createFromObjects(ObjectCollection) - Method in class ObjectCollectionProviderMorphological
-
- createFromObjects(ObjectCollection) - Method in class Scale
-
- createFromObjects(ObjectCollection, Channel) - Method in class BinarySegmentByObject
-
- createFromObjects(ObjectCollection, Channel) - Method in class SegmentChannelByObject
-
- createFromObjects(ObjectCollection) - Method in class ExtendInZ
-
- createFromObjects(ObjectCollection) - Method in class ExtendInZWithinContainer
-
- createFromObjects(ObjectCollection) - Method in class FlattenZ
-
- createFromObjects(ObjectCollection) - Method in class SliceAt
-
- createFromObjects(ObjectCollection) - Method in class RemoveIntersectingVoxels
-
- createFromObjects(ObjectCollection) - Method in class SplitByObjects
-
- createFromObjects(ObjectCollection) - Method in class SplitIntoSquares
-
- createFromObjects(ObjectCollection) - Method in class UnaryWithChannelBase
-
- createFromObjects(ObjectCollection, Channel) - Method in class UnaryWithChannelBase
-
- createFromObjects(ObjectCollection) - Method in class DrawLineAlongConvexHull
-
- createFromObjects(ObjectCollection) - Method in class FillHoles
-
- createFromObjects(ObjectCollection) - Method in class MergeSpatialClusters
-
- createFromObjects(ObjectCollection) - Method in class SplitContourAtSaddlePoints
-
- createFromOutputter(String, OutputterChecked) - Static method in class CSVWriter
-
Creates and starts a CSVWriter if it's allowed, otherwise returns
Optional.empty().
- createFromOutputterWithHeaders(String, OutputterChecked, Supplier<List<String>>, ErrorReporter) - Static method in class CSVWriter
-
- createFromOverlays(ColoredOverlayCollection, IdentifierGetter<Overlay>, IdentifierGetter<ObjectWithProperties>) - Static method in class ObjectDrawAttributesFactory
-
- createFromPath(Path, Logger) - Static method in class ObjectCollectionReader
-
Reads an object-collection from a path (or path prefix) trying different methods to read the
objects.
- createFromPathCached(CheckedSupplier<Path, OperationFailedException>, Logger) - Static method in class ObjectCollectionReader
-
- createFromSource(Channel) - Method in class AutoLocalThreshold
-
- createFromSource(Channel) - Method in class FromChannel
-
- createFromSource(Channel) - Method in class FromChannelBase
-
- createFromSource(Channel) - Method in class SegmentChannel
-
- createFromSource(Channel) - Method in class Threshold
-
- createFromStack(Stack) - Method in class StackProviderUnary
-
- createFromStack(ScaleableBackground, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates the generator with a stack as the background - and with default color green and
flattened across the Z-dimension.
- createFromStack(Optional<ScaleableBackground>, int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates the generator with maybe a stack as the background, or else an empty background - and
with default color green and flattened in Z
- createFromStack(Stack) - Method in class MontageSlices
-
- createFromStack(Stack) - Method in class ColorConverterBase
-
- createFromString(String) - Static method in class AxisConverter
-
Maps a string of x, y, z (case ignored) to a corresponding axis type.
- createFromTupleDuplicate(ReadableTuple3i) - Static method in class Extent
-
Creates from a
ReadableTuple3i representing the sizes in each dimension, where the
tuple
is not used internally.
- createFromTupleReuse(ReadableTuple3i) - Static method in class Extent
-
Creates from a
ReadableTuple3i representing the sizes in each dimension, where the
tuple
is used internally.
- createFromTwoMasks(Mask, Mask) - Method in class And
-
- createFromTwoMasks(Mask, Mask) - Method in class CombineBase
-
Creates masks from some combination of two masks
- createFromTwoMasks(Mask, Mask) - Method in class IfHighLow
-
- createFromTwoMasks(Mask, Mask) - Method in class Or
-
- createFromTwoMasks(Mask, Mask) - Method in class Xor
-
- createGenerator() - Method in class CombineRasterGenerator
-
- createGenerator() - Method in class TextStyle
-
Creates a generator, which produces a drawn string on an image when generated
- createGrayscaleByte(Voxels<UnsignedByteBuffer>) - Static method in class BufferedImageFromVoxels
-
- createGrayscaleShort(Voxels<UnsignedShortBuffer>) - Static method in class BufferedImageFromVoxels
-
- createGroupMap(ConsistentChannelChecker) - Method in class GroupedStackBase
-
Creates a map for the storing an aggregate-data-object for each group.
- createGroupMap(ConsistentChannelChecker) - Method in class ExportImageHistograms
-
- createGroupMap(ConsistentChannelChecker) - Method in class GroupedMeanChannelTask
-
- createHashMapToId() - Method in class MarkCollection
-
- createHeaders(String[], Optional<String>, boolean) - Static method in class LabelHeadersForCSV
-
Creates the label-headers (the headers for columns not associated with features).
- createIdArr() - Method in class MarkCollection
-
- createIdHashMap() - Method in class MarkCollection
-
- createImageDim() - Method in class ReportFeatureForMarks
-
- createImageFormat(String) - Static method in class FileFormatFactory
-
- createInitialization(InitializationContext, ExportSharedObjects) - Method in class DefineOutputter
-
- createInitialization(InitializationContext, Optional<SharedObjects>, Optional<Dictionary>) - Method in class DefineOutputter
-
- createInitializationContext() - Method in class InputBound
-
- createInitializationContext() - Method in class ParametersExperiment
-
- createInitialized(Extent) - Static method in class FromByte
-
Create a buffer of a particular size, that has been initialized.
- createInitialized(Extent) - Static method in class FromFloat
-
Create a buffer of a particular size, that has been initialized.
- createInitialized(Extent) - Static method in class FromInt
-
Create a buffer of a particular size, that has been initialized.
- createInitialized(Extent) - Static method in class FromShort
-
Create a buffer of a particular size, that has been initialized.
- createInitialized(Extent) - Method in interface VoxelsFactoryTypeBound
-
Create a new
Voxels that has been
initialized with memory buffers.
- createInputContext() - Method in class ExecutionArguments
-
Creates an input-context, reusing parameters from the experiment-execution
- createInputsFromFiles(FilesProvider, InputManagerParameters, Function<NamedFile, T>) - Method in class NamedFilesBase
-
Creates a list of inputs from a
FilesProvider which together with the
namer
can create the inputs.
- createIntersectionComplement(ColoredOverlayCollection, ColoredOverlayCollection) - Static method in class ColoredOverlayCollection
-
- createInverted() - Method in class BinaryValuesInt
-
Inverts the values so off becomes on, and vice-versa.
- createKernel() - Method in class DilationContext
-
Creates a kernel for performing the dilation.
- createKernelFactoryNames() - Method in class KernelProposer
-
- createLabelledChannel(BoundedList<T>, Optional<Map<Integer, T>>) - Method in class LabelObjects
-
Creates a channel that contains a unique integer (label) for each element's
object-representation.
- createList(int) - Method in class ColorScheme
-
Creates a sequence of related colors.
- createList(int) - Method in class ColorSchemeUnary
-
- createList(int) - Method in class FromList
-
- createList(int) - Method in class FromSingle
-
- createList(int) - Method in class HSB
-
- createList(int) - Method in class VeryBright
-
- createListBeans(String, HierarchicalConfiguration, Object) - Static method in class BeanListCreator
-
A list of instantiated bean objects from an XML configuration.
- createListChildFeatures() - Method in class Feature
-
Returns a list of Features that exist as bean-properties of this feature, either directly or
in lists.
- createListMembershipWithFlags() - Method in class RegionMap
-
- createManifestDescription() - Method in class AssignmentGenerator
-
- createManifestDescription() - Method in class ChannelGenerator
-
- createManifestDescription() - Method in class ObjectsAsGrayscaleGenerator
-
- createManifestDescription() - Method in class HDF5ObjectsGenerator
-
- createManifestDescription() - Method in class ObjectAsMaskGenerator
-
- createManifestDescription() - Method in class ObjectsAsRGBGenerator
-
- createManifestDescription() - Method in class DrawObjectOnStackGenerator
-
- createManifestDescription() - Method in class ExtractBoundingBoxAreaFromStackGenerator
-
- createManifestDescription() - Method in class RasterGenerator
-
- createManifestDescription() - Method in class RasterGeneratorDelegateToDisplayStack
-
- createManifestDescription() - Method in class RasterGeneratorDelegateToRaster
-
- createManifestDescription() - Method in class RGBTimeSeriesGenerator
-
- createManifestDescription() - Method in class StackGenerator
-
- createManifestDescription(String) - Static method in class CollectionGenerator
-
- createManifestDescription() - Method in class DictionaryGenerator
-
- createManifestDescription() - Method in class SerializedGenerator
-
- createManifestDescription() - Method in class SingleFileTypeGenerator
-
- createManifestDescription() - Method in class SingleFileTypeGeneratorBridge
-
- createManifestDescription() - Method in class CSVGenerator
-
- createManifestDescription() - Method in class StringGenerator
-
- createManifestDescription() - Method in class MarksAsUniqueValueGenerator
-
- createManifestDescription() - Method in class MarksGeneratorBase
-
- createMap(OpenedImageFile, Logger) - Method in class ChannelMap
-
- createMap(OpenedImageFile, Logger) - Method in class Autoname
-
- createMap(OpenedImageFile, Logger) - Method in class FromEntries
-
- createMap(OpenedImageFile, Logger) - Method in class FromMetadata
-
- createMap(OpenedImageFile, Logger) - Method in class SingleChannel
-
- createMapToIndex() - Method in class FeatureNameList
-
Creates a map from the feature-names to their indices in the list.
- createMarkEllipsoidLeastSquares(ObjectMask, Dimensions, boolean, double) - Static method in class EllipsoidFactory
-
Creates a MarkEllipsoid using least-squares fitting to the points on the outline of an
object-mask
- createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>, CreateException>, Dimensions, boolean, double) - Static method in class EllipsoidFactory
-
- createMarkFromPoint(Point3i, int, boolean) - Static method in class MarkConicFactory
-
- createMarkFromPoint(Point3d, int, boolean) - Static method in class MarkConicFactory
-
- CreateMarkFromPoints - Class in org.anchoranalysis.mpp.bean.points
-
- CreateMarkFromPoints() - Constructor for class CreateMarkFromPoints
-
- createMarkFromPoints3f(List<Point3f>) - Static method in class PointListFactory
-
- createMarkFromPoints3i(List<Point3i>) - Static method in class PointListFactory
-
- createMaskOff(Dimensions) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to off.
- createMaskOff(Dimensions, BinaryValuesInt) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to off.
- createMaskOn(Dimensions) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to on.
- createMaskOn(Dimensions, BinaryValuesInt) - Static method in class MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to on.
- createMatcherFile(Path, Optional<InputContextParameters>) - Method in class MatchExtensions
-
- createMatcherFile(Path, Optional<InputContextParameters>) - Method in class MatchGlob
-
- createMatcherFile(Path, Optional<InputContextParameters>) - Method in class MatchRegularExpression
-
- createMatcherFile(Path, Optional<InputContextParameters>) - Method in class PathMatcher
-
- createMerged(ColoredMarks) - Method in class ColoredMarks
-
- createMerged(MarkCollection) - Method in class MarkCollection
-
- createMerged(OverlayCollection) - Method in class OverlayCollection
-
- createMessageForDescription(String) - Method in exception BeanMisconfiguredXMLException
-
- createMessageForDescription(String) - Method in exception LocalisedBeanException
-
- createMessageForDescription(String) - Method in exception AnchorCombinableException
-
Creates a message for the exception from the description.
- createMessageForDescription(String) - Method in exception NamedProviderGetException
-
- createMinusOne() - Method in class Extent
-
Creates a new
Extent with each dimension decreased by one.
- createMockFeatureWithCalculation() - Static method in class MockFeatureWithCalculationFixture
-
Creates a mock-feature (using a mock-FeatureCalculation under the hood) which counts the
number of pixels in an object
- createMockFeatureWithCalculation(ToDoubleFunction<T>) - Static method in class MockFeatureWithCalculationFixture
-
Creates a mock-feature (using a mock-FeatureCalculation under the hood) with a result
calculated using a lambda
- createModelPool(ConcurrencyPlan, Logger) - Method in class SegmentObjectsFromONNXModel
-
- createModelPool(ConcurrencyPlan, Logger) - Method in class SegmentObjectsFromTensorFlowModel
-
- createNamedFeatureList(List<NamedBean<FeatureListProvider<T>>>) - Method in class NamedFeatureStoreFactory
-
- createNamedFeatureProviders(String, TestLoader) - Static method in class FeaturesFromXmlFixture
-
- createNecessaryDirectories(Path) - Static method in class DirectoryCreator
-
Creates necessary directories to make a path to a file valid.
- CreateNew - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
Creates a new channel with all values initialized to a constant (by default zero)
- CreateNew() - Constructor for class CreateNew
-
- CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
-
- CreateNew() - Constructor for class CreateNew
-
- CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
Creates a new empty collection of marks
- CreateNew() - Constructor for class CreateNew
-
- createNewDocument() - Static method in class XMLParser
-
Creates a new XML document.
- createNext(int, int) - Method in interface TableItemArrangement.TableCreator
-
- createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class OverlayMark
-
- createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class OverlayObjectMask
-
- createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class Overlay
-
- createObjects() - Method in class PointsFitterToMark
-
- createObjectsImage(Assignment<ObjectMask>, boolean, AssignmentColorPool) - Method in class DrawColoredObjects
-
Creates an image with the objects colored, as indicated in the class description.
- createOneToMany(Generator<T>, CheckedFunction<S, Stream<T>, ?>) - Static method in class GeneratorBridge
-
Creates a bridge that maps ONE-TO-MANY from source to destination (i.e.
- createOneToOne(Generator<T>, CheckedFunction<S, T, ?>) - Static method in class GeneratorBridge
-
Creates a bridge that maps ONE-TO-ONE from source to destination (i.e.
- createOrderProvider() - Method in class IncreasingIntegers
-
- createOrderProvider() - Method in class IncrementingIntegers
-
- createOrderProvider() - Method in class SequenceType
-
- createOrderProvider() - Method in class StringsWithoutOrder
-
- createOrReuse(Throwable) - Static method in exception InitializeException
-
- createOrReuse(T) - Method in class AlwaysNew
-
- createOrReuse(T) - Method in class CacheAndReuseStrategy
-
- createOrReuse(T) - Method in interface ReplaceStrategy
-
- createOrReuse(T) - Method in class ReuseSingletonStrategy
-
- createOutPathString() - Method in class AppendCsv
-
- createOutPathString() - Method in class AppendDictionary
-
- createOutPathString() - Method in class AppendFilePath
-
- createOutPathString() - Method in class AppendHistogram
-
- createOutPathString() - Method in class AppendMarks
-
- createOutPathString() - Method in class AppendObjects
-
- createOutPathString() - Method in class AppendStack
-
- createOutPathString() - Method in class AppendStackDirect
-
- createOutPathString() - Method in class FilePathAppendBase
-
- createPair(CreateCalculatorHelper, ImageInitialization, CacheTransferSourceCollection) - Method in class MergedPairsFeatures
-
- createPairsUnique() - Method in class RandomCollectionWithAddCriteria
-
- createPairsUnique() - Method in class EnergySavedPairs
-
- createParam(String, boolean) - Method in class PermuteFeatureSequenceInteger
-
- createParameters() - Method in class TouchingVoxels
-
- createParameters(boolean, boolean) - Method in class SurfaceNumberVoxelFaces
-
- createParameters(boolean, boolean) - Method in class SurfaceNumberVoxels
-
- createParameters(boolean, boolean) - Method in class SurfaceNumberVoxelsBase
-
- createPathDeriver(String, String) - Method in class FilePathAppendBase
-
Creates a (rooted) file-path generator for a rootName and a regEx which matches three groups
The first group should correspond to top-level folder for the project The second group should
correspond to the unique name of the dataset.
- createPayloadCalculator() - Method in class MergePairs
-
- createPayloadCalculator() - Method in class MergeToIncreaseObjectFeature
-
- createPayloadCalculator() - Method in class MergeWithFeature
-
Determines the payload for any given or potential vertex
- createPermutedCopies(List<T>, PermuteProperty<S>, PermutationAssigner) - Method in class PermutedCopyCreator
-
Applies a permutation to a copy of each element in a list of beans, updating the custom name
of each bean to reflect the permutation.
- createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeature
-
- createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeatureBase
-
- createPermutedFeaturesFor(Feature<T>) - Method in class PermuteFeatureSequenceInteger
-
- createPolicy() - Method in class ConvertBase
-
- createPrecalc(DrawOverlay, ObjectWithProperties, Dimensions) - Static method in class DrawOverlay
-
- createPrefixerContext() - Method in class ExecutionArguments
-
- createPrioritizer() - Method in class MergePairs
-
- createPrioritizer() - Method in class MergeToIncreaseObjectFeature
-
- createPrioritizer() - Method in class MergeWithFeature
-
Determines the priority (and selection criteria) used to allow merges between neighbors
- createPriority(ObjectVertex, ObjectVertex, Logger) - Method in interface Prioritizer
-
- createRadiiArray() - Method in class ConicBase
-
- createRadiiArray() - Method in class Ellipse
-
- createRadiiArray() - Method in class Ellipsoid
-
- createRadiiArrayResolved(Optional<Resolution>) - Method in class ConicBase
-
- createRadiiArrayResolved(Optional<Resolution>) - Method in class Ellipse
-
- createRadiiArrayResolved(Optional<Resolution>) - Method in class Ellipsoid
-
- createReducedFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair
-
- createRGB(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Extent) - Static method in class BufferedImageFromStack
-
Creates a
BufferedImage from three
Voxels<UnsignedByteBuffer> representing
respectively, red, green, blue color components.
- createRGBStack(Channel, Channel, Channel, VoxelDataType) - Static method in class ThreeChannels
-
- createRoot() - Static method in class ProposerFailureDescription
-
- createRow(String[]) - Method in class ColumnDefinition
-
- createSameSize(ChannelProvider, String, Channel) - Static method in class DimensionsChecker
-
Creates a new channel from a provider, making sure it's the same size as an an existing
channel
- createSameSize(MaskProvider, String, Channel) - Static method in class DimensionsChecker
-
Creates a new channel from a provider, making sure it's the same size as an an existing
channel
- createScaledObject(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in class FromMask
-
- createScaledObject(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in interface ScaledOverlayCreator
-
Creates a scaled-version of the object to use as an overlay..
- createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class OverlayMark
-
- createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class OverlayObjectMask
-
- createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class Overlay
-
- createSecondLevelFromSet(StringSet) - Method in class AddToDefaults
-
- createSecondLevelFromSet(StringSet) - Method in class IgnoreUnderscorePrefixUnless
-
- createSecondLevelFromSet(StringSet) - Method in class NoneExcept
-
- createSecondLevelFromSet(StringSet) - Method in class OutputEnableRulesSpecify
-
- createSecondLevelFromSet(StringSet) - Method in class PermissiveExcept
-
- createSequence(VoxelDataType) - Method in class MultiBufferSized
-
- createSession() - Method in class ObjectCollectionProviderWithFeature
-
- createSet() - Method in class MarkCollection
-
- createSet() - Method in class ColoredOverlayCollection
-
- createSet() - Method in class OverlayCollection
-
- createSetter(AnchorBean<?>) - Method in class PermuteProperty
-
- createSharedStateJob(InputOutputContext) - Method in class ConvertImageFormat
-
Sets a new output-sequence for the series.
- createSharedStateJob(InputOutputContext) - Method in class RasterTask
-
Creates a shared-state for the duration of a particular input-job
- createSharedStateJob(InputOutputContext) - Method in class MovieFromSlices
-
- createSingle(CreateCalculatorHelper, ImageInitialization, BoundReplaceStrategy<FeatureInputSingleObject, CacheAndReuseStrategy<FeatureInputSingleObject>>) - Method in class MergedPairsFeatures
-
- createSingle(T, Function<T, BoundingBox>) - Static method in class BoundedList
-
Creates for a single element using its current bounding-box.
- createSingleStack() - Method in class StackSeries
-
Puts all stacks in the series into a single image stack
- createStack(List<RGBStack>, ChannelFactorySingleType) - Method in class RasterArranger
-
- CreateStackFromBufferedImage - Class in org.anchoranalysis.image.core.bufferedimage
-
- createStackProvider(List<StackProviderWithLabel>, int, boolean, boolean, boolean) - Static method in class TileRasters
-
- createStackSequenceForSeries(int, Logger) - Method in interface StackSequenceInput
-
Creates a supplier of a
TimeSequence of stacks for a particular series number.
- createStackSequenceForSeries(int, Logger) - Method in class ConvertNamedChannelsInputToStack
-
- createStatistics() - Method in class ConcurrentJobMonitor
-
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class MarkRegion
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class CenterSliceBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class GreatestAreaSlice
-
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class IndexedRegionBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class IndexedRegionBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class MaxNonZero
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class SelectSlicesWithIndexBase
-
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class Specific
-
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class Thresholded
-
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSlice
-
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSliceBase
-
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class CenterSliceWindow
-
- createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class AlwaysAllowed
-
- createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class CheckIfAllowed
-
- createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in interface Writer
-
Maybe creates a subdirectory for writing to.
- createSubdirectory(String, ManifestDirectoryDescription, boolean) - Method in class WriterRouterErrors
-
Maybe creates a subdirectory for writing to.
- createSubset(Collection<Integer>) - Method in class ObjectCollection
-
A subset of the collection identified by particular indices.
- createSubset(IntPredicate) - Method in class OverlayCollection
-
- createSubsetFromIDs(IntPredicate) - Method in class ColoredOverlayCollection
-
- createToColorUnselectedObjects() - Static method in class OutlinePreserveRelativeSize
-
Alternative constructor that switches on the coloring of unselected objects by default.
- createTransformerFactory() - Static method in class XMLParser
-
Creates a
TransformerFactory that ignores any DTDs in the document and disables
external entities (to prevent XXE attacks).
- createUninitialised(Dimensions, VoxelDataType) - Method in class ChannelFactory
-
Create a
Channel without initialization with voxel-buffers.
- createUninitialized(Extent) - Static method in class FromByte
-
Create a buffer of a particular size, that has not been initialized.
- createUninitialized(Extent) - Static method in class FromFloat
-
Create a buffer of a particular size, that has not been initialized.
- createUninitialized(Extent) - Static method in class FromInt
-
Create a buffer of a particular size, that has not been initialized.
- createUninitialized(Extent) - Static method in class FromShort
-
Create a buffer of a particular size, that has not been initialized.
- createUninitialized(Extent) - Method in interface VoxelsFactoryTypeBound
-
Create a new
Voxels that has
not yet been initialized with memory buffers.
- createUnsignedByte(Extent, IntFunction<UnsignedByteBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createUnsignedByte(Voxels<UnsignedByteBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createUnsignedByte(BinaryVoxels<UnsignedByteBuffer>) - Method in class ObjectsFromConnectedComponentsFactory
-
Finds the connected-components in unsigned byte voxels.
- createUnsignedByte(Extent) - Static method in class MaxIntensityProjection
-
Creates a buffer for a max-intensity projection for unsigned byte voxels.
- createUnsignedByte(Extent) - Static method in class MeanIntensityProjection
-
Creates a buffer for a mean-intensity projection for unsigned byte voxels.
- createUnsignedByte(Voxels<UnsignedByteBuffer>) - Static method in class VoxelsExtracterFactory
-
- createUnsignedInt(Extent, IntFunction<UnsignedIntBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createUnsignedInt(Voxels<UnsignedIntBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createUnsignedInt(BinaryVoxels<UnsignedIntBuffer>) - Method in class ObjectsFromConnectedComponentsFactory
-
Finds the connected-components in unsigned int voxels.
- createUnsignedInt(Extent) - Static method in class MaxIntensityProjection
-
Creates a buffer for a max-intensity projection for unsigned int voxels.
- createUnsignedInt(Extent) - Static method in class MeanIntensityProjection
-
Creates a buffer for a mean-intensity projection for unsigned int voxels.
- createUnsignedInt(Voxels<UnsignedIntBuffer>) - Static method in class VoxelsExtracterFactory
-
- createUnsignedShort(Extent, IntFunction<UnsignedShortBuffer>) - Static method in class VoxelsArithmeticFactory
-
- createUnsignedShort(Voxels<UnsignedShortBuffer>, int) - Static method in class VoxelsAssignerFactory
-
- createUnsignedShort(Extent) - Static method in class MaxIntensityProjection
-
Creates a buffer for a max-intensity projection for unsigned short voxels.
- createUnsignedShort(Extent) - Static method in class MeanIntensityProjection
-
Creates a buffer for a mean-intensity projection for unsigned short voxels.
- createUnsignedShort(Voxels<UnsignedShortBuffer>) - Static method in class VoxelsExtracterFactory
-
- createVector() - Method in class AxisAlignedUnitVector
-
- createVector() - Method in class DirectionVectorBean
-
Creates a vector in a particular direction
- createVector() - Method in class VectorInDirection
-
- createWithConsoleFallback(OutputterChecked, ExecutionArguments, boolean) - Method in class LoggingDestination
-
Creates a logger for this destination - and if anything goes wrong reporting fallback into
the console.
- createWithEmptyBackground(int, ColorIndex) - Static method in class DrawObjectOnStackGenerator
-
Creates the generator with an empty background - and with default color green and flattened
in Z
- createWithEmptyList() - Static method in class SpecificPathList
-
Factory method for creating the class with an empty list of paths
- createWithLeftUnassigned(ObjectCollection) - Static method in class OverlappingObjects
-
Creates with only left unassigned objects.
- createWithLogFallback(OutputterChecked, MessageLogger, ExecutionArguments, boolean) - Method in class LoggingDestination
-
Creates a logger for this destination - and if anything goes wrong reporting fallback into a
log.
- createWithoutColor(MarkCollection, RegionMembershipWithFlags) - Static method in class OverlayCollectionMarkFactory
-
- createWithoutColor(ObjectCollection, IdentifierGetter<ObjectMask>) - Static method in class OverlayCollectionObjectFactory
-
- createWithoutStacks(InitializationContext) - Static method in class InitializationFactory
-
- createWithPrefix(DirectoryWithPrefix, MultiLevelOutputEnabled, OutputWriteContext, Optional<WriteOperationRecorder>, Optional<MultiLevelRecordedOutputs>, boolean, Optional<Logger>) - Static method in class OutputterChecked
-
Creates a bound output-manager from an existing
OutputManager with a prefix.
- createWithRangeLimits(Iterator<T>, Optional<AxisLimits>) - Method in class PlotIndexBase
-
- createWithRight(ObjectCollection) - Static method in class OverlappingObjects
-
Creates with only right unassigned objects.
- createWithStacks(ProvidesStackInput, InitializationContext) - Static method in class InitializationFactory
-
- createWithXY(double) - Static method in class Resolution
-
Creates with only XY resolution, identical in both dimensions.
- createWithXYAndZ(double, double) - Static method in class Resolution
-
Creates with XY resolution and Z resolution.
- createWriter() - Method in class BioformatsWriter
-
Creates or gets an instance of IFormatWriter which dictates the file format to use
for writing.
- createWriter() - Method in class OMETiff
-
- createWriter() - Method in class OMEXML
-
- createWriter() - Method in class Tiff
-
- createWriter(OutputterChecked) - Method in class ExportReportFeatures
-
- cropRemoveLargerValues(long) - Method in class Histogram
-
- cropRemoveSmallerValues(long) - Method in class Histogram
-
Creates a
Histogram reusing the bins in the current histogram, but with an upper
limit on the total count.
- crossProduct(Vector3d) - Method in class Vector3d
-
- CSVGenerator<T> - Class in org.anchoranalysis.io.generator.tabular
-
- CSVGenerator(String) - Constructor for class CSVGenerator
-
- CSVReader - Class in org.anchoranalysis.io.input.csv
-
Reads a CSV File from the file-system.
- CSVReader(String, boolean) - Constructor for class CSVReader
-
- CSVReader(String, boolean, boolean) - Constructor for class CSVReader
-
- CSVReader.OpenedCSVFile - Class in org.anchoranalysis.io.input.csv
-
- CSVReaderByLine - Class in org.anchoranalysis.io.input.csv
-
Reads a CSV file line-by-line.
- CSVReaderByLine.ProcessCSVLine - Interface in org.anchoranalysis.io.input.csv
-
- CSVReaderException - Exception in org.anchoranalysis.io.input.csv
-
- CSVReaderException(String) - Constructor for exception CSVReaderException
-
- CSVReaderException(Throwable) - Constructor for exception CSVReaderException
-
- CSVReporterAggregated - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
Outputs statistics on current energy / kernel acceptance etc.
- CSVReporterAggregated() - Constructor for class CSVReporterAggregated
-
- CSVReporterBest - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
Outputs a CSV with statistics on the configuration/energy only the best
configuration state changes.
- CSVReporterBest() - Constructor for class CSVReporterBest
-
- CSVReporterUtilities - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- CSVRow - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
A row of the CSV File
- CSVRow(ColumnDefinition) - Constructor for class CSVRow
-
- CSVWriter - Class in org.anchoranalysis.io.generator.tabular
-
- csvWriter(FeatureCSVMetadata) - Method in class FeatureExporterContext
-
- currentStateDescription() - Method in class ConcurrentJobMonitor
-
- currentTemperature() - Method in class AnnealScheme
-
- currentTemperature() - Method in class Geometry
-
- currentTemperature() - Method in class NoAnnealing
-
- customizeExperimentExecutor(ExperimentExecutor, CommandLine) - Method in class LauncherConfig
-
- CutBelowThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
-
This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the
threshold into the bin just below the threshold value
- CutBelowThreshold() - Constructor for class CutBelowThreshold
-
- CVFindContours - Class in org.anchoranalysis.plugin.opencv
-
- CVInit - Class in org.anchoranalysis.plugin.opencv
-
Provides for initialization of the JavaCPP bridge to OpenCV.
- dataType() - Method in class ChannelFactorySingleType
-
- dataType() - Method in class VoxelBuffer
-
Data-type of each voxel in the buffer.
- dataType() - Method in interface VoxelsFactoryTypeBound
-
The data-type of the voxels, as created by this factory.
- dataType() - Method in class Voxels
-
The underlying data-type of the voxels, represented by a
VoxelDataType instance.
- DataTypeMaxIntensity<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity
-
The maximum-intensity allowed by the data-type of the stack.
- DataTypeMaxIntensity() - Constructor for class DataTypeMaxIntensity
-
- DateStyle - Enum in org.anchoranalysis.plugin.io.naming.interval
-
How to style a date in a file-name.
- DebugDependentProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor
-
Executes different processors depending on whether we are in debug mode or not.
- DebugDependentProcessor() - Constructor for class DebugDependentProcessor
-
- DebugModeParameters - Class in org.anchoranalysis.io.input.bean
-
An alternative mode of option where behaviours change.
- DebugModeParameters(Optional<String>) - Constructor for class DebugModeParameters
-
- decode(int) - Static method in class ChainCodesDirection
-
Decodes a chain-code into a point
- decode(List<OnnxTensor>, ImageInferenceContext) - Method in class DecodeMaskRCNN
-
- decode(List<OnnxTensor>, ImageInferenceContext) - Method in class DecodeEAST
-
- decodeConnectedComponentID(int) - Method in class WatershedEncoding
-
- DecodeEAST - Class in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text
-
Extracts text from a RGB image by using the EAST deep neural network model and the ONNX
Runtime.
- DecodeEAST() - Constructor for class DecodeEAST
-
- DecodeLabels<T> - Class in org.anchoranalysis.image.core.object.label
-
Decodes a labelled raster into derived objects or object-like elements.
- DecodeLabels(Voxels<?>, int, int, DecodeLabels.CreateElementFromScaledObject<T>) - Constructor for class DecodeLabels
-
- DecodeLabels.CreateElementFromScaledObject<T> - Interface in org.anchoranalysis.image.core.object.label
-
Creates an element from the scaled-object and its index.
- DecodeMaskRCNN - Class in org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn
-
Decodes the inference output from a Mask-RCNN implementation.
- DecodeMaskRCNN() - Constructor for class DecodeMaskRCNN
-
- DecomposeIntoConnectedComponents - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
-
Ensures each object in a collection is a connected-component, decomposing it if necessary into
multiple objects.
- DecomposeIntoConnectedComponents() - Constructor for class DecomposeIntoConnectedComponents
-
- decrement() - Method in class Counter
-
Decreases the counter by one.
- decrementX() - Method in class KernelPointCursor
-
Decrements the point and associated index by one in the X dimension.
- decrementX() - Method in class Tuple3i
-
Decrements the X component's value by one.
- decrementX(int) - Method in class Tuple3i
-
Decrements the X component's value by a shift.
- decrementY() - Method in class KernelPointCursor
-
Decrements the point and associated index by one in the Y dimension.
- decrementY() - Method in class Tuple3i
-
Decrements the Y component's value by one.
- decrementY(int) - Method in class Tuple3i
-
Decrements the Y component's value by a shift.
- decrementYTwice() - Method in class KernelPointCursor
-
Decrements the point and associated index by two in the Y dimension.
- decrementZ() - Method in class KernelPointCursor
-
Decrements the point by one in the Z dimension.
- decrementZ() - Method in class Tuple3i
-
Decrements the Z component's value by one.
- decrementZ(int) - Method in class Tuple3i
-
Decrements the Z component's value by a shift.
- deepCopy() - Method in class ColorList
-
Creates a new list, containing the duplicates of same elements as the current list.
- deepCopy() - Method in class RandomCollectionWithAddCriteria
-
- deepCopy() - Method in class EnergyTotal
-
- deepCopy() - Method in class MarksWithEnergyBreakdown
-
- deepCopy() - Method in class MarksWithTotalEnergy
-
Make a deep copy (except the energyScheme which is reused).
- deepCopy() - Method in class VoxelizedMarksWithEnergy
-
Creates a deep-copy of the marks
- deepCopy() - Method in class EnergySavedAll
-
- deepCopy() - Method in class EnergySavedInd
-
- deepCopy() - Method in class EnergySavedPairs
-
- deepCopy() - Method in class ColoredMarks
-
- deepCopy() - Method in class MarkCollection
-
- deepCopy() - Method in class AggIDCounter
-
- deepCopy() - Method in class Aggregator
-
- Default - Class in org.anchoranalysis.io.bioformats.bean.options
-
- Default() - Constructor for class Default
-
- DEFAULT_CHARACTER - Static variable in class Divider
-
The default character used in the divider, if not otherwise specified in the constructor.
- DEFAULT_COLOR_SET_GENERATOR - Static variable in class ColoredBase
-
- DEFAULT_FUNC_NUM_PIXELS - Static variable in class MockFeatureWithCalculationFixture
-
- DEFAULT_IMAGE_INPUT_NAME - Static variable in class MultiInput
-
- DEFAULT_NUMBER_CHARACTERS_IN_BANNER - Static variable in class Divider
-
The default total nubmer of characters to use in the divier, if not otherwise specified in
the constructor.
- DefaultChildCacheFinder - Class in org.anchoranalysis.feature.session.cache.finder
-
The default strategy for finding children by always directly taking (or creating a child-cache)
as necessary.
- defaultColorIndexFor(int) - Method in class OutputWriteSettings
-
- defaultExperimentOrCustom(CommandLine, Path) - Static method in class ExperimentFactory
-
Chooses either a path to the default-experiment or a path to a custom experiment.
- DefaultInstance - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates a default bean-instance is available.
- defaultOutputs() - Method in class InputOutputExperiment
-
- defaultOutputs() - Method in class OutputExperiment
-
If specified, default rules for determine which outputs are enabled or not.
- defaultOutputs() - Method in class Task
-
If specified, default rules for determine which outputs are enabled or not.
- defaultOutputs() - Method in class SegmentIntoMarks
-
If specified, default rules for determine which outputs are enabled or not.
- defaultOutputs() - Method in class AggregateAnnotations
-
- defaultOutputs() - Method in class CompareAnnotations
-
- defaultOutputs() - Method in class ExportFeatures
-
- defaultOutputs() - Method in class ConvertImageFormat
-
- defaultOutputs() - Method in class ExportImageHistograms
-
- defaultOutputs() - Method in class GroupedMeanChannelTask
-
- defaultOutputs() - Method in class ImageAssignLabel
-
- defaultOutputs() - Method in class ScaleImage
-
- defaultOutputs() - Method in class SegmentInstanceWithModel
-
- defaultOutputs() - Method in class ExtractSlice
-
- defaultOutputs() - Method in class MovieFromSlices
-
- defaultOutputs() - Method in class CombineCSV
-
- defaultOutputs() - Method in class CopyFiles
-
- defaultOutputs() - Method in class ConvertNamedChannels
-
- defaultOutputs() - Method in class Develop
-
- defaultOutputs() - Method in class ExportReportFeatures
-
- defaultOutputs() - Method in class ExportObjectsAsCroppedImages
-
- defaultOutputs() - Method in class ExportObjectsFromCSV
-
- defaultOutputs() - Method in class SegmentMarksFromImage
-
- defaultOutputs() - Method in class SegmentWithMarkedPointProcess
-
- Define - Class in org.anchoranalysis.bean.define
-
A bean where the definitions of many different
NamedBeans can be specified.
- Define() - Constructor for class Define
-
- Define<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
-
Specifies a list of features directly without assigning any custom-naming.
- Define(List<Feature<T>>) - Constructor for class Define
-
- Define() - Constructor for class Define
-
- DefineAdder - Interface in org.anchoranalysis.bean.define.adder
-
Indicates that an object can add one or more items to a
Define.
- DefineAdderBean - Class in org.anchoranalysis.bean.define.adder
-
- DefineAdderBean() - Constructor for class DefineAdderBean
-
- DefineAdderWithPrefixBean - Class in org.anchoranalysis.bean.define.adder
-
- DefineAdderWithPrefixBean() - Constructor for class DefineAdderWithPrefixBean
-
- DefineAddException - Exception in org.anchoranalysis.bean.define
-
Called when a bean fails to be added to a
Define.
- DefineAddException(String) - Constructor for exception DefineAddException
-
Creates with a message only.
- DefineAddException(Throwable) - Constructor for exception DefineAddException
-
Creates with a cause only.
- DefineAddException(String, Throwable) - Constructor for exception DefineAddException
-
Creates with a message and cause.
- DefinedNamed<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
-
Specifies features via a list of names and associated with features.
- DefinedNamed() - Constructor for class DefinedNamed
-
- DefineFactory - Class in org.anchoranalysis.bean.define
-
- DefineFactory() - Constructor for class DefineFactory
-
- DefineOutputter - Class in org.anchoranalysis.mpp.segment.bean.define
-
After using applying a
Define on inputs, output produced entities (images, histograms,
objects etc.)
- DefineOutputter() - Constructor for class DefineOutputter
-
- DefineOutputter.Processor<T> - Interface in org.anchoranalysis.mpp.segment.bean.define
-
- DefineOutputterWithEnergy - Class in org.anchoranalysis.plugin.mpp.bean.define
-
Like a
Define but outputs also an energy-stack.
- DefineOutputterWithEnergy() - Constructor for class DefineOutputterWithEnergy
-
- DefineOutputterWithEnergy.ProcessWithEnergyStack<T,S> - Interface in org.anchoranalysis.plugin.mpp.bean.define
-
Processes the energy-stack.
- DefineSingle<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
-
Specifies a single feature directly without assigning any custom-naming.
- DefineSingle() - Constructor for class DefineSingle
-
- DefineSingle(Feature<T>) - Constructor for class DefineSingle
-
- delegate() - Method in class ReadOptionsDelegate
-
- delete(Path) - Method in interface AnnotationDeleter
-
Deletes all files at this path (or any other paths derived from this one.
- delete(Path) - Method in class DualMarksAnnotationDeleter
-
- delete(Path) - Method in class SimpleAnnotationDeleter
-
- deriveBufferedImage() - Method in class DisplayStack
-
- deriveContext(InputOutputContext) - Method in class ExportFeaturesStyle
-
- DerivedObject - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
-
- DerivedObject() - Constructor for class DerivedObject
-
- DeriveElementsFromSequencedDirectory<T> - Class in org.anchoranalysis.io.manifest.directory.sequenced
-
Derives elements of type T from a directory containing a sequence of files.
- DeriveElementsFromSequencedDirectory(SequencedDirectory) - Constructor for class DeriveElementsFromSequencedDirectory
-
- deriveExtent() - Method in class ObjectCollectionProviderMorphological
-
- deriveFrom(Supplier<Optional<Path>>, boolean) - Method in class DerivePath
-
Derives a new path from an existing path.
- deriveFrom(Path, boolean) - Method in class DerivePath
-
Derives a new path from an existing path.
- deriveFrom(Path, boolean) - Method in class Constant
-
- deriveFrom(Path, boolean) - Method in class InsertRegExGroups
-
- deriveFrom(Path, boolean) - Method in class JoinRegExGroups
-
- deriveFrom(Path, boolean) - Method in class Replace
-
- deriveFrom(Path, boolean) - Method in class Rooted
-
- deriveFrom(Path, boolean) - Method in class CollapseFileName
-
- deriveFrom(Path, boolean) - Method in class RemoveTrailingDirectory
-
- deriveFromDelegate(FeatureInputSingleObject, ObjectCollection) - Method in class CalculateIntersecting
-
- deriveFromDelegate(T, U) - Method in class CalculateInputFromDelegate
-
- DeriveFromPair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
Embeds each feature in a
FeatureDeriveFromPair feature (
first,
second or
merge) and prepends with a string.
- DeriveFromPair() - Constructor for class DeriveFromPair
-
- deriveIndex(String) - Static method in class RGBChannelNames
-
Derives the index of a channel for a channel name.
- deriveInput(Stack, Optional<double[]>) - Method in class SegmentObjectsFromONNXModel
-
- deriveInput(Stack, Optional<double[]>) - Method in class SegmentObjectsFromTensorFlowModel
-
- deriveInputsStartBatch(ObjectCollection, EnergyStack, boolean, Logger) - Method in class CombineObjectsForFeatures
-
Derives a list of inputs (i.e.
- deriveLabels(String, Optional<String>, int) - Method in interface LabelsForInput
-
Calculates labels for a given input (and index).
- deriveName(File, FileNamerContext) - Method in class FileNamer
-
A name for a file.
- deriveName(List<File>, FileNamerContext) - Method in class FileNamer
-
Derives a list of names (associated with each file) for some files.
- deriveName(List<File>, FileNamerContext) - Method in class FileNamerIndependent
-
- deriveName(File, Optional<Path>, int) - Method in class FileNamerIndependent
-
- deriveName(File, Optional<Path>, int) - Method in class FromOutputName
-
- deriveName(List<File>, FileNamerContext) - Method in class IfRelativeToDirectory
-
- deriveName(File, Optional<Path>, int) - Method in class LastDirectories
-
- deriveName(File, Optional<Path>, int) - Method in class NormalizedPath
-
- deriveName(List<File>, FileNamerContext) - Method in class PatternSpan
-
- deriveName(File, Optional<Path>, int) - Method in class RegExMatcher
-
- deriveName(File, Optional<Path>, int) - Method in class RelativeToDirectory
-
- deriveName(List<File>, FileNamerContext) - Method in class RemoveExtension
-
- deriveName(List<File>, FileNamerContext) - Method in class SubsetRangeIfRequested
-
- deriveNames() - Method in class FeatureList
-
Derives the names of the features.
- deriveNameUnique(List<File>, FileNamerContext) - Method in class FileNamer
-
- deriveObject(BoundingBox) - Method in class PredicateAtCorner
-
- deriveObject(BoundingBox) - Method in class PredicateImplementation
-
- deriveObject(BoundingBox) - Method in interface VoxelsPredicate
-
Creates an object-mask for all the voxels inside the bounding-box satisfying the predicate.
- deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class Mark
-
- deriveObjects(Dimensions, RegionMembershipWithFlags) - Method in class MarkCollection
-
- DerivePath - Class in org.anchoranalysis.io.input.bean.path
-
Derives a path from an existing path.
- DerivePath() - Constructor for class DerivePath
-
- derivePath(DerivePath, Path) - Static method in class PathFromGenerator
-
- DerivePathException - Exception in org.anchoranalysis.io.input.path
-
- DerivePathException(String) - Constructor for exception DerivePathException
-
- DerivePathException(Throwable) - Constructor for exception DerivePathException
-
- DerivePathException(String, Throwable) - Constructor for exception DerivePathException
-
- derivePointsLocal() - Method in class ObjectMask
-
Creates a list of all on voxels as points, using local coordinates i.e.
- deriveRootedPath(Path, String, boolean, boolean) - Static method in class RootedFilePathUtilities
-
- deriveRotationMatrix() - Method in class Orientation
-
Derives a
RotationMatrix that can be applied to rotate an entity
anti-clockwise to the current orientation.
- deriveRotationMatrix() - Method in class Orientation2D
-
- deriveRotationMatrix() - Method in class Orientation3DEulerAngles
-
- deriveRotationMatrix() - Method in class OrientationAxisAngle
-
- deriveRotationMatrix() - Method in class OrientationRotationMatrix
-
- deriveScalingFactor(int, int) - Static method in class Scaler
-
Calculates a scaling-factor (for one dimension) by doing a floating point division of two
integers.
- deriveScore(double, double, FeatureResultSupplier) - Method in class GaussianCumulative
-
- deriveScore(double, double, FeatureResultSupplier) - Method in class StatisticalBase
-
Derive scores given the value, mean and standard-deviation
- deriveScore(double, double, FeatureResultSupplier) - Method in class ZScore
-
- deriveScoreFromVoxel(int) - Method in class CalculateLevelBase
-
- deriveScoreFromVoxel(int) - Method in class NormalizeByConstant
-
- deriveScoreFromVoxel(int) - Method in class NormalizeByMax
-
- deriveScoreFromVoxel(int) - Method in class SingleChannel
-
- deriveStack(boolean) - Method in class DisplayStack
-
Derives a
Stack from the display-stack that will be converted to 8-bit if necessary.
- deriveStatistic(DoubleArrayList) - Method in class MeanAcrossObjects
-
- deriveStatistic(DoubleArrayList) - Method in class ObjectAggregationBase
-
- deriveStatistic(DoubleArrayList) - Method in class QuantileAcrossObjects
-
- deriveSubdirectory(String, ManifestDirectoryDescription, boolean) - Method in class Outputter
-
- deriveSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class OutputterChecked
-
Derives a bound-output-manager for a (possibly newly created) subdirectory of the existing
manager
- deriveSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class ElementOutputter
-
Derives a bound-output-manager for a (possibly newly created) subdirectory of the existing
manager
- deriveUnsignedBytePredicate() - Method in interface PredicateTwoBytes
-
- deriveUnsignedByteProcessor() - Method in interface PredicateTwoBytes
-
- describe() - Method in class GraphWithoutPayload
-
Describes the graph in a multi-line string.
- describe(boolean) - Method in class GraphWithPayload
-
Describes the graph in a multi-line string.
- describe() - Method in interface SelectParam
-
A string that can be displayed to the user to describe this particular SelectParam.
- describe() - Method in class UseDefaultManager
-
- describe() - Method in class ProposerFailureDescription
-
- describe() - Method in class DescribeGraph
-
Generates a string describing the entire graph (vertices and edges)
- describe() - Method in class SummarizerImageMetadata
-
- describe() - Method in class SummarizerInputFromManager
-
- describe() - Method in class ExtensionCount
-
- describe() - Method in class FilePathPattern
-
- describe() - Method in class FileSizeStatistics
-
- describe() - Method in class Summarizer
-
A string summarizing this item.
- describe() - Method in class SummarizerAggregate
-
- describe() - Method in class SummarizerCount
-
- describe() - Method in class SummarizerListMultiline
-
- describe() - Method in class SummarizerSplitMoreThan
-
- describe(String) - Method in class FrequencyMap
-
- describeAcceptedClasses() - Method in class AssignerMatchClass
-
- describeAcceptedClasses() - Method in interface InitializationParameterAssigner
-
A string describing which classes of initialization-parameters are accepted or not.
- describeBean() - Method in class AnchorBean
-
A (maybe longer) description identifying the bean and perhaps its key parameters.
- describeBean() - Method in class Feature
-
- describeBean() - Method in class FeatureList
-
- describeBean() - Method in class Overlay
-
- describeBean() - Method in class CombineRasterGenerator
-
- describeBean() - Method in class BoundMinMax
-
- describeBean() - Method in class BoundUnitless
-
- describeBean() - Method in class BoundRotation2D
-
- describeBean() - Method in class BoundRotation3D
-
- describeBean() - Method in class MarkWithIdentifierFactory
-
- describeBean() - Method in class AddCriteriaPair
-
- describeBean() - Method in class MarkPairCollection
-
- describeBean() - Method in class FeedbackReceiverList
-
- describeBean() - Method in class FromMarkProposer
-
- describeBean() - Method in class FromSerializedMarks
-
- describeBean() - Method in class SimulatedAnnealing
-
- describeChildren() - Method in class AnchorBean
-
Generates a string describing the children of the current bean.
- describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class DescribeGraph
-
Generates a string to describe a potential merge
- describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class GraphLogger
-
- describeExecutionTimes(RunningSum, RecordedExecutionTimes, long) - Static method in class DescribeExecutionTimeStatistics
-
Describes how long operations took to complete en aggregate with related-statistics.
- DescribeExecutionTimeStatistics - Class in org.anchoranalysis.experiment.time
-
Generates report of the execution-times of different operations.
- DescribeGraph - Class in org.anchoranalysis.plugin.image.object.merge
-
Logs descriptions of the graph
- DescribeGraph(NeighborGraph, boolean) - Constructor for class DescribeGraph
-
Constructor
- describeLast() - Method in class Kernel
-
- describeLast() - Method in class KernelBirth
-
- describeLast() - Method in class KernelBirthAndKill
-
- describeLast() - Method in class KernelDeath
-
- describeLast() - Method in class KernelExchange
-
- describeLast() - Method in class KernelInitialMarksFromPartition
-
- describeLast() - Method in class KernelInitialMarksProposed
-
- describeLast() - Method in class KernelInitialMarksVoxelized
-
- describeLast() - Method in class KernelMerge
-
- describeLast() - Method in class KernelReplace
-
- describeLast() - Method in class KernelSplit
-
- describeMarks(MarkCollection) - Method in class EnergySavedInd
-
- describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class DescribeGraph
-
- describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class GraphLogger
-
- describeNoun() - Method in class BitDepth
-
- describeNoun() - Method in class ImageSize
-
- describeNoun() - Method in class NumberChannels
-
- describeNoun() - Method in class SummarizerImageMetadata
-
- describeOrientation(BiConsumer<String, String>) - Method in class Orientation
-
Consumes descriptive human-readable name-value pairs to describe the current orientation.
- describeOrientation(BiConsumer<String, String>) - Method in class Orientation2D
-
- describeOrientation(BiConsumer<String, String>) - Method in class Orientation3DEulerAngles
-
- describeOrientation(BiConsumer<String, String>) - Method in class OrientationAxisAngle
-
- describeOrientation(BiConsumer<String, String>) - Method in class OrientationRotationMatrix
-
- describeParameters() - Method in class Feature
-
A human-readable description of the parameterization of the bean.
- describeParameters() - Method in class Constant
-
- describeParameters() - Method in class AsSingle
-
- describeParameters() - Method in class ForSpecificAxis
-
- describeParameters() - Method in class Count
-
- describeParameters() - Method in class RatioThreshold
-
- describeParameters() - Method in class BoundingBoxAlongAxisBase
-
- describeParameters() - Method in class IntensityMeanShellBase
-
- describeParameters() - Method in class UnitsWithinRange
-
- describeParameters() - Method in class BoundingBoxExtent
-
- describeParameters() - Method in class AsMark
-
- describeParameters() - Method in class AsObject
-
- describeParameters() - Method in class Intensity
-
- describeParameters() - Method in class MeanIntensityDifference
-
- describeParameters() - Method in class MaxOverlapRatio
-
- describeParameters() - Method in class HOGFeature
-
- describeParameters() - Method in class InvertedMax
-
- describeParameters() - Method in class CompareWithRange
-
- describeParameters() - Method in class CompareWithRangeFeature
-
- describeParameters() - Method in class RangeCompareBase
-
- describeParameters() - Method in class RangeCompareFromScalars
-
- describeParameters() - Method in class StatisticalBase
-
- describePropertiesFriendly() - Method in class MorphologicalIterations
-
A string that uniquely identifies all properties in the bean, but friendly to humans
- describePropertyValue(T) - Method in class PermuteProperty
-
Describes a particular property-value in a unique but human-readable way.
- describePropertyValue(Double) - Method in class PermutePropertyDoubleSet
-
- describePropertyValue(Double) - Method in class PermutePropertySequenceDouble
-
- describePropertyValue(Integer) - Method in class PermutePropertySequenceInteger
-
- describePropertyValue(String) - Method in class PermutePropertyStringSet
-
- describeTo(boolean) - Method in class TypedEdge
-
Describes the edge by showing the to vertex, and optionally the payload.
- description() - Method in class MutableDirectory
-
A description of this directory for the manifest.
- description(String, String) - Static method in class DirectoryMatch
-
- description(String, String) - Static method in class FileMatch
-
Match a file whose manifest-description has a specific function and type.
- description(String) - Static method in class FileMatch
-
Match a file whose manifest-description has a specific function.
- description(String, String, String) - Static method in class FileMatch
-
Match a file whose manifest-description has either of two specific function and a specific
type.
- descriptionAndOutputName(String, String, String, String) - Static method in class FileMatch
-
Match a file whose manifest-description has either of two specific function and a specific
type and whose output-name matches a specific value.
- descriptionForList(String) - Method in class FeatureFromList
-
Derive a string description of all the items of the list concatenated together.
- descriptionLong() - Method in class Feature
-
A long human-readable description of the feature and some or all of its parameterization.
- descriptionLong() - Method in class Constant
-
- descriptionLong() - Method in class Reference
-
- descriptionLong() - Method in class Sum
-
- descriptionLong() - Method in class Intensity
-
- descriptionLong() - Method in class AbsoluteValue
-
- descriptionLong() - Method in class Divide
-
- descriptionLong() - Method in class InvertedMax
-
- descriptionLong() - Method in class Multiply
-
- descriptionLong() - Method in class MeanGeometric
-
- descriptionLong() - Method in class NormalizedRange
-
- descriptionLong() - Method in class Range
-
- descriptionLong() - Method in class WithValueBase
-
- DescriptionMatch - Class in org.anchoranalysis.io.manifest.finder.match
-
- descriptiveIdentifier() - Method in interface FileFormat
-
An identifier that describes the format, that is meaningful to the end-user.
- descriptiveIdentifier() - Method in enum ImageFileFormat
-
- descriptiveIdentifier() - Method in enum NonImageFileFormat
-
- DescriptiveNameContainsImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
- DescriptiveNameContainsImageLabeller() - Constructor for class DescriptiveNameContainsImageLabeller
-
- DeserializationFailedException - Exception in org.anchoranalysis.core.serialize
-
When a deserialization operation fails.
- DeserializationFailedException(String) - Constructor for exception DeserializationFailedException
-
Creates with a message, but without a cause.
- DeserializationFailedException(Exception) - Constructor for exception DeserializationFailedException
-
Creates with a cause, but without a message.
- DeserializationFailedException(String, Throwable) - Constructor for exception DeserializationFailedException
-
Creates with message and cause.
- deserialize(Path, Logger) - Method in interface Deserializer
-
Deserializes a representation of an object stored on the filesystem.
- deserialize(Path, Logger) - Method in class DictionaryDeserializer
-
- deserialize(Path, Logger) - Method in class ObjectInputStreamDeserializer
-
- deserialize(Path, Logger) - Method in class XStreamDeserializer
-
- deserialize(Path, Logger) - Method in class MarkCollectionDeserializer
-
- DeserializedManifest - Class in org.anchoranalysis.plugin.io.manifest
-
A manifest after being deserialized from the file-system.
- DeserializedManifest(File, ManifestDeserializer, Logger) - Constructor for class DeserializedManifest
-
- deserializeManifest(File, Logger) - Method in interface ManifestDeserializer
-
- deserializeManifest(File, Logger) - Method in class SimpleManifestDeserializer
-
- Deserializer<T> - Interface in org.anchoranalysis.core.serialize
-
Creates an object from a serialized representation on the file-system.
- DestinationChannelForIndex - Interface in org.anchoranalysis.io.bioformats
-
Selects a destination-channel for the byte-copier, given an index
- destinationPath(File, DirectoryWithPrefix, int, CopyContext<T>) - Method in class CopyFilesNaming
-
Returns the output path (destination to to be copied to) for a given single file.
- destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<AnonymizeSharedState>) - Method in class Anonymize
-
- destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<ClusterMembership>) - Method in class ClusterByTimestamp
-
- destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<T>) - Method in class CopyFilesNaming
-
Calculates the relative-output path (to be appended to destDir)
- destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class CopyFilesNamingOne
-
- destinationPathRelative(Path) - Method in class CopyFilesNamingOne
-
- destinationPathRelative(Path, String) - Method in class FilterWithRegularExpression
-
- destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class OutputPrefixWithExtension
-
- destinationPathRelative(File, DirectoryWithPrefix, int, CopyContext<NoSharedState>) - Method in class PreserveName
-
- destinationPathRelative(Path) - Method in class RegularExpressionBase
-
- destinationPathRelative(Path, String) - Method in class RegularExpressionBase
-
- destinationPathRelative(Path) - Method in class RemoveWhitespace
-
- destinationPathRelative(Path, String) - Method in class SubstituteRegularExpression
-
- destinationSize - Variable in class ConvertTo
-
The total number of elements (whatever the destination type is) in the destination buffer.
- determineChannelNames(IFormatReader) - Method in class Default
-
- determineChannelNames(IFormatReader) - Method in class ReadOptions
-
A list of channel-names, if available.
- determineChannelNames(IFormatReader) - Method in class ReadOptionsDelegate
-
- determineChannelNames(IFormatReader) - Method in class SwitchChannelTime
-
- determineCost() - Method in class MergeCandidate
-
Merges
- determineEnabledOutputs(RecordedOutputsWithRules) - Method in class OutputManager
-
Determines which outputs are enabled or not.
- determineInputType(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class FeatureInputType
-
Finds a common input-type for two classes, throwing an exception if the two types aren't
compatible.
- determineInputType(List<Feature<T>>) - Static method in class FeatureInputType
-
Finds a common input-type for classes in the list, throwing an exception if any two types
aren't compatible.
- determineOrientationCorrection(Path) - Static method in class OrientationReader
-
Determines the needed correction to orientation for the voxels if an EXIF orientation tag is
present.
- determineOrientationCorrection(Metadata) - Static method in class OrientationReader
-
Determines the needed correction to orientation for the voxels if an EXIF orientation tag is
present.
- Develop - Class in org.anchoranalysis.plugin.mpp.experiment.bean.define
-
Derives various types of outputs (images, histograms etc.) from
MultiInputs.
- Develop() - Constructor for class Develop
-
- dictionaries() - Method in class ImageInitialization
-
- Dictionary - Class in org.anchoranalysis.core.value
-
Collection of parameters represented by key-value pairs.
- Dictionary() - Constructor for class Dictionary
-
Creates empty, with no parameters.
- dictionary() - Method in class MarksInitialization
-
- dictionary() - Method in class MultiInput
-
- DICTIONARY_IDENTIFIER - Static variable in class ImageInitialization
-
- DictionaryBean<T> - Class in org.anchoranalysis.bean.shared.dictionary
-
- DictionaryBean() - Constructor for class DictionaryBean
-
- DictionaryCondition - Class in org.anchoranalysis.plugin.image.bean.dictionary
-
Checks if a value in a
Dictionary is equal to an expected-value.
- DictionaryCondition() - Constructor for class DictionaryCondition
-
- dictionaryDeriver() - Method in class MarkProposerStrategy
-
- DictionaryDeserializer<T> - Class in org.anchoranalysis.core.serialize
-
Deserializes a
Dictionary from a file-system representation as a Java properties file.
- DictionaryDeserializer() - Constructor for class DictionaryDeserializer
-
- DictionaryForImageCreator - Class in org.anchoranalysis.mpp.feature.energy.scheme
-
- DictionaryForImageCreator(EnergyScheme, SharedFeatures, Logger) - Constructor for class DictionaryForImageCreator
-
- DictionaryGenerator - Class in org.anchoranalysis.io.generator.serialized
-
Writes the contents of a
Dictionary to the file-system as XML.
- DictionaryGenerator(String) - Constructor for class DictionaryGenerator
-
- DictionaryInitialization - Class in org.anchoranalysis.bean.shared.dictionary
-
Initialization parameters that provide a named-mapping to
Dictionarys.
- DictionaryInitialization(SharedObjects) - Constructor for class DictionaryInitialization
-
- dictionaryInitialization() - Method in class ImageInitialization
-
- DictionaryProvider - Class in org.anchoranalysis.bean.shared.dictionary
-
- DictionaryProvider() - Constructor for class DictionaryProvider
-
- DictionaryProviderReference - Class in org.anchoranalysis.bean.shared.dictionary
-
References a particular
Dictionary in shared-object-space.
- DictionaryProviderReference() - Constructor for class DictionaryProviderReference
-
- Difference - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- Difference() - Constructor for class Difference
-
- DifferenceCalculateLevelStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
Similar to
Difference but calculates the width as the standard-deviation of the histogram
- DifferenceCalculateLevelStandardDeviation() - Constructor for class DifferenceCalculateLevelStandardDeviation
-
- differenceFrom(Path, Path) - Static method in class PathDifference
-
Finds the difference between a path and a base.
- dilate(boolean, Optional<Extent>) - Method in class BoundedVoxels
-
Grow bounding-box by 1 pixel in all directions.
- dilate(ObjectMask, Optional<Extent>, boolean, int, boolean) - Static method in class MorphologicalDilation
-
Dilates an
ObjectMask, growing the bounding-box as necessary.
- dilate(BinaryVoxels<UnsignedByteBuffer>, int, DilationContext) - Static method in class MorphologicalDilation
-
Performs a morphological dilation operation.
- Dilate - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
-
Performs a
dilation morphological operation on
BinaryVoxels.
- Dilate() - Constructor for class Dilate
-
- Dilate - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
-
Dilates each object in the collection, growing bounding-boxes as necessary in relevant
dimensions.
- Dilate() - Constructor for class Dilate
-
- DilationContext - Class in org.anchoranalysis.image.voxel.kernel.morphological
-
Additional parameters for influencing a morphologicla dilation opperation.
- DilationContext(OutsideKernelPolicy, boolean, boolean, Optional<Predicate<Point3i>>) - Constructor for class DilationContext
-
Create without a post-condition.
- DilationContext(OutsideKernelPolicy, boolean, boolean, Optional<Predicate<Point3i>>, Optional<AcceptIterationPredicate>) - Constructor for class DilationContext
-
Create with a post-condition.
- DilationKernel - Class in org.anchoranalysis.image.voxel.kernel.morphological
-
Morphological dilation with a 3x3 or 3x3x3 kernel size.
- DilationKernel(boolean) - Constructor for class DilationKernel
-
Creates with a type of neighborhood.
- dimensionIndexFor(Axis) - Static method in class AxisConverter
-
A corresponding index representing for the dimension an
Axis represents.
- dimensions() - Method in class EnergyStack
-
The image-dimensions associated with the energy-stack.
- dimensions() - Method in class EnergyStackWithoutParameters
-
The dimensions of all channels in the stack.
- dimensions() - Method in class FeatureInputDimensions
-
The dimensions of the associated image.
- dimensions() - Method in class FeatureInputEnergy
-
- dimensions() - Method in class Channel
-
The size and voxel-resolution of the channel.
- Dimensions - Class in org.anchoranalysis.image.core.dimensions
-
The size of an image (in voxels), together with the image resolution.
- Dimensions(int, int, int) - Constructor for class Dimensions
-
Construct with an explicit extent and no resolution.
- Dimensions(ReadableTuple3i) - Constructor for class Dimensions
-
Construct with an explicit extent and no resolution.
- Dimensions(Extent) - Constructor for class Dimensions
-
Construct with an explicit extent and no resolution.
- Dimensions(Extent, Optional<Resolution>) - Constructor for class Dimensions
-
- dimensions(Dimensions) - Method in enum OrientationChange
-
A
Dimensions that describes {code dimensions} after the orientation change.
- dimensions() - Method in class Mask
-
The size and voxel-resolution of the channel.
- dimensions() - Method in class DisplayStack
-
The dimensions of all channels in the stack.
- dimensions() - Method in class RGBStack
-
The dimensions of all channels in the stack.
- dimensions() - Method in class Stack
-
The dimensions of all channels in the stack.
- dimensions() - Method in class FeatureInputImageMetadata
-
- dimensions(int, Logger) - Method in class NamedChannelsInput
-
Dimensions of a particular series.
- dimensions(Logger) - Method in interface NamedChannelsForSeries
-
- dimensions(Logger) - Method in class NamedChannelsForSeriesConcatenate
-
- dimensions(Logger) - Method in class NamedChannelsForSeriesMap
-
- dimensions() - Method in class ObjectsAsGrayscaleGenerator
-
The dimensions associated with the objects (assumed to be constant across any change in
element).
- dimensions() - Method in class TimeSequence
-
- dimensions() - Method in class FeatureInputMarkCollection
-
- dimensions() - Method in class ProposerContext
-
- dimensions() - Method in class TransformationContext
-
- DimensionsChecker - Class in org.anchoranalysis.plugin.image.channel
-
- DimensionsCreator - Class in org.anchoranalysis.io.bioformats
-
- DimensionsCreator(IMetadata) - Constructor for class DimensionsCreator
-
- dimensionsForSeries(int, Logger) - Method in interface OpenedImageFile
-
The
Dimensions associated with a particular series.
- dimensionsForSeries(int, Logger) - Method in class OpenedMultiFile
-
- dimensionsOptional() - Method in class FeatureInputEnergy
-
The image-dimensions associated with the energy-stack, if it exists.
- DimensionsProvider - Class in org.anchoranalysis.image.bean.provider
-
- DimensionsProvider() - Constructor for class DimensionsProvider
-
- dimensionsRequired() - Method in class FeatureInputEnergy
-
The image-dimensions associated with the energy-stack, or an exception if no energy-stack
exists.
- DirectAssignMode<S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
-
Directly assigns a state for every optimisation step
- DirectAssignMode() - Constructor for class DirectAssignMode
-
- DirectAssignMode(ExtractScoreSize<S>) - Constructor for class DirectAssignMode
-
- DirectionVector - Class in org.anchoranalysis.spatial.orientation
-
A vector indicating a direction in space.
- DirectionVector() - Constructor for class DirectionVector
-
Creates with each dimension's value set to 0.
- DirectionVector(Tuple3d) - Constructor for class DirectionVector
-
Creates reusing
Tuple3d internally for the dimension's values.
- DirectionVector(double, double, double) - Constructor for class DirectionVector
-
Creates for a particular value in each dimension.
- DirectionVector(Axis) - Constructor for class DirectionVector
-
Creates a direction aligned to a particular axis.
- DirectionVectorBean - Class in org.anchoranalysis.image.bean.spatial.direction
-
- DirectionVectorBean() - Constructor for class DirectionVectorBean
-
- directory() - Method in class InputsWithDirectory
-
The directory associated with the inputs.
- DirectoryCreator - Class in org.anchoranalysis.core.system.path
-
Creates necessary directories on a file-system to make a path valid.
- DirectoryDepth - Class in org.anchoranalysis.plugin.io.bean.input.files.provider
-
Lists all directories to a certain depth
- DirectoryDepth() - Constructor for class DirectoryDepth
-
- DirectoryMatch - Class in org.anchoranalysis.io.manifest.finder.match
-
- DirectoryStructure - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer
-
Reuses the directories between a path and its root to form the output - and also the filename.
- DirectoryStructure() - Constructor for class DirectoryStructure
-
- DirectoryWithPrefix - Class in org.anchoranalysis.io.output.path.prefixer
-
- DirectoryWithPrefix(Path) - Constructor for class DirectoryWithPrefix
-
- DirectoryWithPrefix(Path, String, String) - Constructor for class DirectoryWithPrefix
-
- disableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class OutputEnabledDelta
-
Assigns additional outputs to disable.
- DiscardOutliers - Class in org.anchoranalysis.plugin.image.bean.object.filter.collective
-
Calculates features values for all objects, and discards any object less than
quantile - (minRatio * stdDev)
- DiscardOutliers() - Constructor for class DiscardOutliers
-
- DisplayStack - Class in org.anchoranalysis.image.core.stack
-
Stack that contains 1 or 3 channels so that we and display it as either grayscale or as an RGB
unsigned 8-bit image, respectively.
- DisplayStackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator
-
Writes a display-stack to the filesystem.
- DisplayStackGenerator(String, boolean) - Constructor for class DisplayStackGenerator
-
Creates the generator.
- distance(BoundingBox, BoundingBox, boolean) - Static method in class BoundingBoxDistance
-
- distance(Point2d) - Method in class Point2d
-
The square of the Euclidean distance between this point and another
Point2d.
- distance(Point3d) - Method in class Point3d
-
The Euclidean distance between this point and another
Point3d.
- distance(Point3f) - Method in class Point3f
-
The Euclidean distance between this point and another.
- distance(Point3i) - Method in class Point3i
-
The Euclidean distance between this point and another.
- DistanceCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
-
- DistanceCondition(Optional<UnitValueDistance>, boolean, MessageLogger) - Constructor for class DistanceCondition
-
- DistanceIndex - Class in org.anchoranalysis.plugin.mpp.contour.distance
-
A distance, and the index the point came from
- DistanceIndex(int, int) - Constructor for class DistanceIndex
-
- DistanceIndexTwice - Class in org.anchoranalysis.plugin.mpp.contour.distance
-
A distance, and the two indices the point came from
- DistanceIndexTwice(int, int, int) - Constructor for class DistanceIndexTwice
-
- distanceMax(Point3i) - Method in class Point3i
-
The maximum distance across any individual axis to another point.
- DistancePhysical - Class in org.anchoranalysis.image.bean.unitvalue.distance
-
- DistancePhysical() - Constructor for class DistancePhysical
-
- distanceSquared(Point2d) - Method in class Point2d
-
The square of the Euclidean distance between this point and another
Point2d.
- distanceSquared(Point3d) - Method in class Point3d
-
The square of the Euclidean distance between this point and another
Point3d.
- distanceSquared(Point3i) - Method in class Point3d
-
The square of the Euclidean distance between this point and another
Point3i.
- distanceSquared(Point3f) - Method in class Point3f
-
The square of the Euclidean distance between this point and another.
- distanceSquared(Point3i) - Method in class Point3i
-
The square of the Euclidean distance between this point and another
Point3i.
- distanceSquared(Point3d) - Method in class Point3i
-
The square of the Euclidean distance between this point and another
Point3d.
- distanceSquaredTo(Point3i) - Method in class LevelResult
-
- DistanceToContiguousPath - Class in org.anchoranalysis.plugin.mpp.contour.distance
-
- DistanceTransform3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
-
Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
- DistanceTransform3D() - Constructor for class DistanceTransform3D
-
- DistanceTransformForEachObject3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
-
Like
DistanceTransform3D but applies the distance transform separately for each object in
a collection.
- DistanceTransformForEachObject3D() - Constructor for class DistanceTransformForEachObject3D
-
- DistanceVoxels - Class in org.anchoranalysis.image.bean.unitvalue.distance
-
- DistanceVoxels(double) - Constructor for class DistanceVoxels
-
- DistanceVoxels() - Constructor for class DistanceVoxels
-
- div(int) - Method in class AggIDCounter
-
- div(AggIDCounter) - Method in class AggIDCounter
-
- Divide<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- Divide() - Constructor for class Divide
-
- divideBy(int) - Method in interface VoxelsArithmetic
-
Divides the value of all voxels by a scalar constant.
- divideBy(int) - Method in class Aggregator
-
- divideBy(int) - Method in class Tuple3d
-
Arithmetically divide values across each dimension.
- divideBy(double) - Method in class Tuple3d
-
Arithmetically divide values across each dimension.
- divideBy(int) - Method in class Tuple3i
-
Arithmetically divide by a value across each dimension.
- DivideByConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- DivideByConstant() - Constructor for class DivideByConstant
-
- divideByZeroReplace(double, double, double) - Static method in class DoubleUtilities
-
Replaces a value with a constant if the denominator is 0.
- Divider - Class in org.anchoranalysis.core.log
-
Creates a line of text that span a certain width with a repeated character, optionally containing
a label.
- Divider() - Constructor for class Divider
-
A banner using dashes.
- Divider(int) - Constructor for class Divider
-
A banner using dashes, with a particular number of characters.
- Divider(char) - Constructor for class Divider
-
A banner using a particular repeated character.
- Divider(char, int) - Constructor for class Divider
-
A banner using a particular repeated character.
- doDuplicate(PointListBase) - Method in class PointListBase
-
- doesClassInheritFromAny(Class<? extends InputFromManager>) - Method in class InputTypesExpected
-
Does the childclass inherit from any one of expected input-types
- doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class BinaryKernelMorphological
-
Does a particular neighboring-point satisfy the conditions.
- doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class DilationKernel
-
- doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class ErosionKernel
-
Checks whether a particular neighbor voxel qualifies to make the current voxel an outline
voxel.
- doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class OutlineKernel
-
Checks whether a particular neighbor voxel qualifies to make the current voxel an outline
voxel.
- doesNeighborQualify(boolean, KernelPointCursor, Supplier<UnsignedByteBuffer>, int) - Method in class OutlineKernelNeighborMatchValue
-
Checks whether a particular neighbor voxel qualifies to make the current voxel an outline
voxel.
- doesNeighborVoxelQualify(Point3i) - Method in class CountKernel
-
Whether a particular neighboring voxel is accepted or not.
- doesNeighborVoxelQualify(Point3i) - Method in class CountKernelNeighborhood
-
- doesNeighborVoxelQualify(Point3i) - Method in class CountKernelNeighborhoodMask
-
- doesPathExist(String) - Method in class TestLoader
-
Does a resource exist with a particular folderPath + fileName.
- doesPathExist(String, String) - Method in class TestLoader
-
Does a resource exist with a particular folderPath + fileName.
- doFind(Manifest) - Method in interface Finder
-
- doFind(Manifest) - Method in class FinderExperimentFileDirectories
-
- doFind(Manifest) - Method in class FinderSingleDirectory
-
- doFind(Manifest) - Method in class FinderSingleFile
-
- doJobOnInput(InputBound<T, S>) - Method in class Task
-
Performs the task on a particular input.
- doJobOnInput(InputBound<S, NoSharedState>) - Method in class HelloWorld
-
- doJobOnInput(InputBound<AnnotationWithStrategy<S>, AggregateSharedState>) - Method in class AggregateAnnotations
-
- doJobOnInput(InputBound<AnnotationComparisonInput<ProvidesStackInput>, ComparisonSharedState<T>>) - Method in class CompareAnnotations
-
- doJobOnInput(InputBound<T, FeatureExporter<S>>) - Method in class ExportFeatures
-
- doJobOnInput(InputBound<ProvidesStackInput, GroupedSharedState<S, T>>) - Method in class GroupedStackBase
-
- doJobOnInput(InputBound<ProvidesStackInput, SharedStateFilteredImageOutput<T>>) - Method in class ImageAssignLabel
-
- doJobOnInput(InputBound<NamedChannelsInput, S>) - Method in class RasterTask
-
- doJobOnInput(InputBound<StackSequenceInput, NoSharedState>) - Method in class ScaleImage
-
- doJobOnInput(InputBound<StackSequenceInput, SharedStateSegmentInstance<T>>) - Method in class SegmentInstanceWithModel
-
- doJobOnInput(InputBound<NamedChannelsInput, SharedStateSelectedSlice>) - Method in class ExtractSlice
-
- doJobOnInput(InputBound<FileInput, CSVWriter>) - Method in class CombineCSV
-
- doJobOnInput(InputBound<FileWithDirectoryInput, RecordingCounter<T>>) - Method in class CopyFiles
-
- doJobOnInput(InputBound<T, Summarizer<S>>) - Method in class SummarizeBase
-
- doJobOnInput(InputBound<T, SharedStateRememberConverted<U, S>>) - Method in class ConvertNamedChannels
-
- doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class Develop
-
- doJobOnInput(InputBound<ManifestCouplingDefinition, NoSharedState>) - Method in class ExportReportFeaturesFromManifest
-
- doJobOnInput(InputBound<MultiInput, CSVWriter>) - Method in class ExportReportFeaturesFromMulti
-
- doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class ExportObjectsAsCroppedImages
-
- doJobOnInput(InputBound<FromCSVInput, FromCSVSharedState>) - Method in class ExportObjectsFromCSV
-
- doJobOnInput(InputBound<MultiInput, ExperimentState>) - Method in class SegmentMarksFromImage
-
- doOperation(VoxelizedMarkMemo, Dimensions) - Method in class PxlListOperationFromMark
-
- doStack(InputBound<NamedChannelsInput, NoSharedState>, OutputSequenceIndexed<Stack, String>, int, int, InputOutputContext) - Method in class ConvertImageFormat
-
- doStack(InputBound<NamedChannelsInput, S>, U, int, int, InputOutputContext) - Method in class RasterTask
-
Processes one stack from a series.
- doStack(InputBound<NamedChannelsInput, OutputSequenceIncrementing<Stack>>, NoSharedState, int, int, InputOutputContext) - Method in class MovieFromSlices
-
- dotProduct(Tuple3d) - Method in class Tuple3d
-
- DotProductOrientationToVector - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
-
- DotProductOrientationToVector() - Constructor for class DotProductOrientationToVector
-
- double3DFromFloat(Point2f) - Static method in class PointConverter
-
- DoubleBiPredicate - Interface in org.anchoranalysis.math.relation
-
- doubleFromFloat(Point2f) - Static method in class PointConverter
-
- doubleFromFloat(Point3f) - Static method in class PointConverter
-
- doubleFromInt(Point2i) - Static method in class PointConverter
-
Convert a
Point2i to a
Point3d using
0 as the value of the Z-axis
component.
- doubleFromInt(ReadableTuple3i) - Static method in class PointConverter
-
- DoubleList - Class in org.anchoranalysis.bean.primitive
-
A bean defining a list of
Doubles.
- DoubleList(Double...) - Constructor for class DoubleList
-
Constructs with one or more values added to the list.
- DoubleListFactory - Class in org.anchoranalysis.bean.xml.factory.primitive
-
- DoubleListFactory() - Constructor for class DoubleListFactory
-
- DoubleSet - Class in org.anchoranalysis.bean.primitive
-
A bean defining a set of
Doubles.
- DoubleSet(Double...) - Constructor for class DoubleSet
-
Constructs with one or more values added to the set.
- DoubleSet() - Constructor for class DoubleSet
-
- DoubleSetFactory - Class in org.anchoranalysis.bean.xml.factory.primitive
-
- DoubleSetFactory() - Constructor for class DoubleSetFactory
-
- DoubleUtilities - Class in org.anchoranalysis.math.arithmetic
-
Utilities for arithmetic operations involving type double.
- DrawColoredObjects - Class in org.anchoranalysis.annotation.io.assignment.generator
-
Outlines or completely fills in each
ObjectMask with a color.
- DrawColoredObjects(DisplayStack, boolean, int) - Constructor for class DrawColoredObjects
-
- DrawCroppedObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.rgb
-
- DrawCroppedObjectsGenerator(DrawObject, DisplayStack, ColorIndex) - Constructor for class DrawCroppedObjectsGenerator
-
- DrawLineAlongConvexHull - Class in org.anchoranalysis.plugin.imagej.bean.object.provider
-
Draws a lines between successive points on the convex-hull of an object.
- DrawLineAlongConvexHull() - Constructor for class DrawLineAlongConvexHull
-
- DrawObject - Class in org.anchoranalysis.overlay.bean
-
Draws an object-mask on a RGB-stack
- DrawObject() - Constructor for class DrawObject
-
- DrawObjectOnStackGenerator - Class in org.anchoranalysis.image.io.stack.output.box
-
Creates images of object(s) drawn on a background only in a local region around their bounding
box.
- DrawObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.rgb
-
Generates stacks of RGB images using a
DrawObject to draw objects on a background.
- DrawOverlay - Class in org.anchoranalysis.overlay.writer
-
Draws an overlay onto a RGB-stack, including precalculated overlays.
- DrawOverlay() - Constructor for class DrawOverlay
-
- dropKey() - Method in exception NamedFeatureCalculateException
-
Removes any feature-name from the exception.
- dropZ() - Method in class Point3d
-
Creates a new point with identical x and y values, but with z set to 0.
- DualMarks - Interface in org.anchoranalysis.annotation.mark
-
Two mark-collections, one considered accepted and the other rejected.
- DualMarksAnnotation<T> - Class in org.anchoranalysis.annotation.mark
-
An annotation that consists of two sets of marks, accepted and rejected.
- DualMarksAnnotation() - Constructor for class DualMarksAnnotation
-
- DualMarksAnnotationAsObjects<T> - Class in org.anchoranalysis.plugin.annotation.bean.comparer
-
- DualMarksAnnotationAsObjects() - Constructor for class DualMarksAnnotationAsObjects
-
- DualMarksAnnotationDeleter - Class in org.anchoranalysis.annotation.io.mark
-
- DualMarksAnnotationDeleter() - Constructor for class DualMarksAnnotationDeleter
-
- DualMarksAnnotationReader<T> - Class in org.anchoranalysis.annotation.io.mark
-
- DualMarksAnnotationReader(boolean) - Constructor for class DualMarksAnnotationReader
-
- DualMarksAnnotationWriter<T> - Class in org.anchoranalysis.annotation.io.mark
-
- DualMarksAnnotationWriter() - Constructor for class DualMarksAnnotationWriter
-
- DualMarksAnnotationWriter(boolean) - Constructor for class DualMarksAnnotationWriter
-
- DualPathPredicates - Class in org.anchoranalysis.io.input.path.matcher
-
A Predicate<Path for both a file and a directory.
- DualPathPredicates(Predicate<Path>, Predicate<Path>) - Constructor for class DualPathPredicates
-
- DualStack - Class in org.anchoranalysis.mpp.segment.optimization
-
Stores an
EnergyStack together with a background stack.
- DualStack(EnergyStack) - Constructor for class DualStack
-
Creates to infer a background from the energy-stack.
- DualStack(EnergyStack, DisplayStack) - Constructor for class DualStack
-
- DualState<T> - Class in org.anchoranalysis.mpp.segment.optimization
-
Remembers the current state of type T and some best state (which was once set from the current
state)
- DualState() - Constructor for class DualState
-
- DualVoxelizedMarks - Class in org.anchoranalysis.plugin.mpp.segment.optimization
-
- DualVoxelizedMarks(VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Constructor for class DualVoxelizedMarks
-
- DualWriterOperationRecorder - Class in org.anchoranalysis.io.manifest.operationrecorder
-
- DualWriterOperationRecorder(WriteOperationRecorder, WriteOperationRecorder) - Constructor for class DualWriterOperationRecorder
-
- duplicate() - Method in class RGBColor
-
Creates a deep-copy of the current object.
- duplicate() - Method in class Dictionary
-
Deep-copy of existing dictionary.
- duplicate() - Method in class SharedFeatures
-
A deep copy of the current instance.
- duplicate() - Method in class NamedFeatureStore
-
Deep-copies the store, including duplicating each feature.
- duplicate() - Method in class Channel
-
A deep-copy.
- duplicate() - Method in class Mask
-
Deep-copies the object.
- duplicate() - Method in class ObjectWithProperties
-
Deep copies the current instance.
- duplicate() - Method in class RGBStack
-
A deep copy.
- duplicate() - Method in class StackNotUniformSized
-
A deep-copy.
- duplicate() - Method in class MergedPairsFeatures
-
Immutably creates entirely new duplicated features
- duplicate() - Method in class BinaryVoxels
-
Deep-copy of the object, including duplicating voxel buffers in memory.
- duplicate() - Method in class BoundedVoxels
-
A deep-copy of the current structure.
- duplicate() - Method in class VoxelBuffer
-
Creates a deep copy of the current object, including deep-copying the associated buffer.
- duplicate() - Method in class ObjectCollection
-
- duplicate() - Method in class ObjectMask
-
Creates a deep-copy of the current object-mask.
- duplicate() - Method in class Voxels
-
A deep-copy.
- duplicate() - Method in class IndexableOutputNameStyle
-
- duplicate() - Method in class IntegerSuffixOutputNameStyle
-
- duplicate() - Method in class OutputNameStyle
-
Deep copy the current object.
- duplicate() - Method in class SimpleOutputNameStyle
-
- duplicate() - Method in class StringSuffixOutputNameStyle
-
- duplicate() - Method in class WithoutOutputNameStyle
-
- duplicate() - Method in class RunningSum
-
Deep-copy.
- duplicate() - Method in class Histogram
-
Creates a deep-copy of the current object.
- duplicate() - Method in class EigenvalueAndVector
-
Creates a deep-copy of the current object.
- duplicate() - Method in class ImageMoments
-
Creates a deep-copy of the current object.
- duplicate() - Method in class Bound
-
- duplicate() - Method in class BoundDegrees
-
- duplicate() - Method in class BoundPhysicalExtent
-
- duplicate() - Method in class BoundUnitless
-
- duplicate() - Method in class Circle
-
- duplicate() - Method in class Ellipse
-
- duplicate() - Method in class Ellipsoid
-
- duplicate() - Method in class Sphere
-
- duplicate() - Method in class Mark
-
- duplicate() - Method in class LineSegment
-
- duplicate() - Method in class PointList
-
- duplicate() - Method in class Polygon
-
- duplicate() - Method in class PolygonCurve
-
- duplicate() - Method in class RotatableBoundingBox
-
- duplicate() - Method in interface VoxelizedMark
-
- duplicate() - Method in class AxisLimits
-
- Duplicate - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
- Duplicate() - Constructor for class Duplicate
-
- Duplicate - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
- Duplicate() - Constructor for class Duplicate
-
- Duplicate - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Duplicates (deep copy) an object-collection.
- Duplicate() - Constructor for class Duplicate
-
- duplicate() - Method in class ContiguousVoxelPath
-
- duplicate() - Method in class RotationMatrix
-
Deep-copy of the current rotation-matrix.
- duplicateBean() - Method in class AnchorBean
-
Creates a new bean that deep-copies every property value.
- duplicateBean() - Method in class Define
-
- duplicateBean() - Method in class DoubleList
-
Duplicate the bean.
- duplicateBean() - Method in class DoubleSet
-
Duplicate the bean.
- duplicateBean() - Method in class IntegerList
-
Duplicate the bean.
- duplicateBean() - Method in class IntegerSet
-
Duplicate the bean.
- duplicateBean() - Method in class StringList
-
Duplicate the bean.
- duplicateBean() - Method in class StringSet
-
Duplicate the bean.
- duplicateBean() - Method in class RGBColorBean
-
- duplicateChangeExtent(Extent) - Method in class Dimensions
-
Deep-copies the current object, but assigns a different
Extent.
- duplicateChangeName(String) - Method in class Feature
-
- duplicateChangeResolution(Optional<Resolution>) - Method in class Dimensions
-
Deep-copies the current object, but assigns a different
Resolution.
- duplicateChangeZ(int) - Method in class Dimensions
-
Deep-copies the current object, but assigns a different size for the Z-dimension.
- duplicateChangeZ(int) - Method in class Extent
-
Creates a copy of the current
Extent with the value for the Z-dimension changed.
- duplicateChangeZ(int) - Method in class Point3i
-
- duplicateChangeZ(int) - Method in interface ReadableTuple3i
-
Creates a copy of the current tuple, but with a different Z-component value.
- duplicateDeep() - Method in class Stack
-
Performs a deep copy of the stack, so that all channels are duplicated.
- duplicateForNewThread() - Method in interface FeatureTableCalculator
-
Makes a copy of the feature-store for a new thread.
- duplicateForNewThread() - Method in class PairsTableCalculator
-
- duplicateForNewThread() - Method in class SingleTableCalculator
-
- duplicateFresh() - Method in class VoxelizedMarkMemo
-
- duplicateShallow() - Method in class FeatureInitialization
-
A shallow-copy of the current initialization.
- duplicateShallow() - Method in class FeatureNameList
-
Shallow copy of the current instance.
- duplicateShallow() - Method in class Stack
-
Performs a shallow copy of the stack, so that all channels are reused.
- duplicateShallow() - Method in class ObjectCollection
-
Shallow copy of objects.
- GaussianBlur2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
-
- GaussianBlur2D() - Constructor for class GaussianBlur2D
-
- GaussianCumulative<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics
-
- GaussianCumulative() - Constructor for class GaussianCumulative
-
- GaussianSampler - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
Samples from a Gaussian distribution whose parameters are determined by a
Dictionary.
- GaussianSampler() - Constructor for class GaussianSampler
-
- generalWriteException(Class<T>, Path, Exception) - Static method in class WriterErrorMessageHelper
-
- generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class DrawCroppedObjectsGenerator
-
- generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class DrawObjectsGenerator
-
- generateBackground(ObjectCollectionWithProperties, Either<Dimensions, DisplayStack>) - Method in class ObjectsAsRGBGenerator
-
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in interface AddCriteria
-
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaEnergyPair
-
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaNever
-
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaPair
-
- generateIntersectingObjects(int, int, boolean) - Static method in class IntersectingCircleObjectsFixture
-
Generates a number of circles that intersect and don't intersect
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class PeriodicSubdirectoryReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class KernelIterDescriptionSerializerPeriodicReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class ObjectSerializerPeriodicReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class TextFileMarksReporter
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class TiffTimeSeries
-
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksPeriodicReporter
-
- generateMasks(ObjectCollectionWithProperties) - Method in class DrawCroppedObjectsGenerator
-
- generateMasks(ObjectCollectionWithProperties) - Method in class DrawObjectsGenerator
-
- generateMasks(ObjectCollectionWithProperties) - Method in class ObjectsAsRGBGenerator
-
- generateNormal(double, double) - Method in interface RandomNumberGenerator
-
Generates a Gaussian (Normal) random variable with particular parameterization.
- generateNormal(double, double) - Method in class RandomNumberGeneratorMersenne
-
- generatePoisson(double) - Method in interface RandomNumberGenerator
-
Generates a Poisson random variable with particular parameterization.
- generatePoisson(double) - Method in class RandomNumberGeneratorMersenne
-
- generateProperties(Optional<Resolution>) - Method in class Ellipse
-
- generateProperties(Optional<Resolution>) - Method in class Ellipsoid
-
- generateProperties(Optional<Resolution>) - Method in class Mark
-
- generateProperties(Optional<Resolution>) - Method in class MarkWithPosition
-
- generateProperties(Optional<Resolution>) - Method in class OverlayMark
-
- generateProperties(Optional<Resolution>) - Method in class OverlayObjectMask
-
- generateProperties(Optional<Resolution>) - Method in class Overlay
-
- GenerateString - Class in org.anchoranalysis.image.io.bean.stack.combine
-
- GenerateString(String) - Constructor for class GenerateString
-
- GenerateString() - Constructor for class GenerateString
-
- GenerateToMatchObjects - Class in org.anchoranalysis.plugin.image.bean.color.provider
-
Generates colors to match the size of an object-collection.
- GenerateToMatchObjects() - Constructor for class GenerateToMatchObjects
-
- GenerateUniqueParameterization - Interface in org.anchoranalysis.bean
-
Objects that must implement well-defined equals() and hashCode() methods and also
generate a name uniquely identifying the class and all parameterization.
- generator() - Static method in class ObjectCollectionWriter
-
- Generator<T> - Interface in org.anchoranalysis.io.generator
-
A class that writes a particular type of object(s) to the filesystem.
- GeneratorBridge<S,T> - Class in org.anchoranalysis.io.generator
-
Exposes a Generator<T> as if it was an Generator<S>.
- GeneratorOutputter - Class in org.anchoranalysis.image.io.stack.output.generator
-
Settings and methods for writing to the filesystem from a generator.
- Geometry - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
-
- Geometry() - Constructor for class Geometry
-
- Geometry(double, double) - Constructor for class Geometry
-
- get() - Method in interface Provider
-
Gets or creates an object of type T.
- get() - Method in class DictionaryProviderReference
-
- get() - Method in class CachedSupplier
-
- get(K) - Method in class LRUCache
-
Get a value, calculating if necessary, and caching the result.
- get(int) - Method in interface ColorIndex
-
The color for a particular index.
- get(int) - Method in class ColorIndexModulo
-
- get(int) - Method in class ColorList
-
- get(int) - Method in class SingleColor
-
- get() - Method in interface CheckedSupplier
-
Applies a supplier like with Supplier.get().
- get() - Method in interface StoreSupplier
-
Gets the object being supplied to the store.
- get(Progress) - Method in class CachedProgressingSupplier
-
- get(Progress) - Method in interface CheckedProgressingSupplier
-
Applies a supplier like with Supplier.get().
- get() - Static method in class ProgressIgnore
-
Gets a singleton instance of the class.
- get() - Method in class Define
-
- get() - Method in class DefinedNamed
-
- get() - Method in class DefineSingle
-
- get(int) - Method in class FeatureList
-
Returns the element at the specified position in this list.
- get() - Method in class PrependName
-
- get() - Method in class FeatureProviderDefine
-
- get() - Method in class FeatureProviderReference
-
- get() - Method in interface FeatureCalculationInput
-
The underlying feature-input.
- get(int) - Method in class LabelledResultsVector
-
The result of a feature-calculation stored at a particular index.
- get(int) - Method in class FeatureNameList
-
Gets a name corresponding to a particular position.
- get(int) - Method in class ResultsVector
-
The result of a feature-calculation stored at a particular index.
- get(int) - Method in class ResultsVectorList
-
- get() - Method in interface CacheSupplier
-
- get() - Method in class SessionInputSequential
-
- get(int) - Method in class NamedFeatureStore
-
Gets a feature at a particular position.
- get(String) - Method in class NamedFeatureStore
-
Gets a feature corresponding to a particular name.
- get(int) - Method in class BoundingBoxesOnPlane
-
- get(int, int) - Method in class TableItemArrangement
-
- get() - Method in class ChannelProviderBinary
-
- get() - Method in class ChannelProviderTernary
-
- get() - Method in class ChannelProviderUnary
-
- get() - Method in class HistogramProviderUnary
-
- get() - Method in class MaskProviderUnary
-
- get() - Method in class ObjectCollectionProviderUnary
-
- get() - Method in class ArrangeRaster
-
- get() - Method in class StackProviderUnary
-
- get(int) - Method in class ObjectCollectionWithProperties
-
Get an item at a particular index.
- get(Progress) - Method in interface NamedStacksSupplier
-
- get() - Method in class GenerateString
-
- get() - Method in class TileWithLabels
-
- get(String) - Method in class NamedEntries
-
- get(Progress) - Method in interface TimeSequenceSupplier
-
- get(int) - Method in class StackSeries
-
- get(int) - Method in class TimeSequence
-
- get(VoxelDataType) - Method in class VoxelDataTypeFactoryMultiplexer
-
Multiplexes one of the factories according to data-type
- get(int) - Method in class ObjectCollection
-
Get an
ObjectMask at a particular position in the collection.
- get(int) - Method in interface DestinationChannelForIndex
-
- get() - Method in class ReadFromFile
-
- get() - Method in class FilePathProviderReference
-
- get() - Method in class FromFiles
-
- get() - Method in interface PathSupplier
-
- get(int) - Method in class DeriveElementsFromSequencedDirectory
-
- get(int) - Method in interface SupplierAtIndex
-
- get() - Method in class FinderDictionary
-
- get() - Method in class FinderFileAsText
-
- get() - Method in class FinderSerializedObject
-
- get() - Method in interface SerializedObjectSupplier
-
- get(Optional<String>) - Method in class InputOutputContextSubdirectoryCache
-
Gets (from the cache if it's already there) a context for a subdirectory of given-name
- get() - Method in interface ElementSupplier
-
Gets/creates the element to be written.
- get() - Method in interface ElementWriterSupplier
-
- get(int) - Method in class RunningSumCollection
-
An individual item in the collection.
- get(int) - Method in class ImageMoments
-
Get an eigenvalue and corresponding eigenvector for a particular axis.
- get(int) - Method in class MarksWithTotalEnergy
-
- get(int) - Method in class EnergySavedInd
-
- get(String) - Method in class EnergySchemeSet
-
- get(int) - Method in class MemoList
-
- get(int) - Method in class UpdatableMarksList
-
- get(int) - Method in class IndexByChannel
-
- get(String) - Method in interface MultiInputSubMap
-
Returns null if non-existent
- get(String) - Method in class OperationMap
-
- get(String) - Method in class StackWithMap
-
- get(int) - Method in class MarkCollection
-
- get(int) - Method in class AggIDCounter
-
- get(int) - Method in class WeightedKernelList
-
- get(int) - Method in class ColoredOverlayCollection
-
- get(int) - Method in class OverlayCollection
-
- get(T, int) - Method in interface GetForSeries
-
- get(String) - Method in class GroupedAnnotationLabels
-
- get() - Method in class FromDimensionsBase
-
- get() - Method in class FromInput
-
- get() - Method in class FromStack
-
- get() - Method in class FromMaskBase
-
- get() - Method in class Reference
-
- get() - Method in class ScoreVoxels
-
- get() - Method in class Concatenate
-
- get() - Method in class GenerateToMatchObjects
-
- get() - Method in class FromChannel
-
- get() - Method in class GuessDimensions
-
- get() - Method in class SpecifyDimensions
-
- get() - Method in class FromChannel
-
- get() - Method in class Reference
-
- get() - Method in class FromStackChannel
-
- get() - Method in class FromChannelBase
-
- get() - Method in class FromDimensionsBase
-
- get() - Method in class Reference
-
- get() - Method in class Concatenate
-
- get() - Method in class ConnectedComponentsFromMask
-
- get() - Method in class Empty
-
- get() - Method in class IfParamEqual
-
- get() - Method in class FromMask
-
- get() - Method in class MergeTwoCollectionsItemwise
-
- get() - Method in class Permute
-
- get() - Method in class Reference
-
- get() - Method in class ReferenceOrElse
-
- get() - Method in class SegmentStack
-
- get() - Method in class WithChannelBase
-
- get() - Method in class ColoredBase
-
- get() - Method in class ThreeChannels
-
- get() - Method in class Concatenate
-
- get() - Method in class FromChannelOrMask
-
- get() - Method in class FromInput
-
- get() - Method in class PlotHistogram
-
- get() - Method in class Reference
-
- get() - Method in class IntensityMoments
-
- get() - Method in class DeriveFromPair
-
- get() - Method in class FeatureListProviderAggregatePair
-
- get() - Method in class PermuteFeatureBase
-
- get(int) - Method in class ListWithThumbnails
-
- get() - Method in class PriorityQueueIndexRangeDownhill
-
- get(T) - Method in class FileLabelMap
-
- get() - Method in class DeserializedManifest
-
- get() - Method in class FeatureListProviderLDAClassifier
-
- get() - Method in class FeatureListProviderSVMClassifier
-
- get() - Method in class MarkBoundsDefine
-
- get() - Method in class MarkBoundsReference
-
- get() - Method in class FromMarks
-
- get() - Method in class CreateNew
-
- get() - Method in class FromSingleMark
-
- get() - Method in class PointsFromObjects
-
- get() - Method in class Reference
-
- get() - Method in class ReferenceOrEmpty
-
- get() - Method in class ScaleXY
-
- get() - Method in class CreateEllipse
-
- get() - Method in class RequireFeatureRelationThreshold
-
- get() - Method in class RetrieveSingleMarkOnly
-
- get(int) - Method in class ContiguousVoxelPath
-
- get(String) - Method in class IndexedCSVRows
-
- get(String) - Method in class MapGroupToRow
-
- get() - Method in class HOGDescriptor
-
- get() - Method in interface FeatureResultSupplier
-
- get() - Method in class FitPointsFromObjects
-
- get(int) - Method in class BoundedList
-
Gets a particular element.
- getAboveMaxValue() - Method in class RangeCompareBase
-
Constant to return if outside the range (above the maximum allowed)
- getAcceptAll() - Method in class Aggregator
-
- getAcqusitionTime() - Method in class ImageMetadata
-
A timestamp, if available, of when the image was first physically created by the
camera/device.
- getAcqusitionTime() - Method in class ImageTimestampsAttributes
-
A timestamp, if available, of when the image was first physically created by the
camera/device.
- getAdd() - Method in class VisualizeOnBackground
-
- getAddCriteria() - Method in class RandomCollectionWithAddCriteria
-
- getAdditionalBackgrounds() - Method in class MarkProposerStrategy
-
Additional background-stacks that are possible to use while annotating.
- getAdditionalChannels() - Method in class MultiInputManagerQuick
-
Additional channels other than the main one, which are located in the main raster file
- getAdditionalChannels() - Method in class NamedChannelsQuick
-
Additional channels other than the main one, which are located in the main raster file
- getAdditionalPropertyPaths() - Method in class PermuteProperty
-
Additional property paths that are also changed, together with propertyPath.
- getAddSum() - Method in class GradientBaseAddSum
-
Added to all gradients (so we can store negative gradients)
- getAdjacentChannels() - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file adjacent to the main raster file
- getAfterPreoperation() - Method in class OverlappingObject
-
After pre-operation but before scaling
- getAggInterval() - Method in class ReporterInterval
-
- getAggIntervalLog10() - Method in class ReporterInterval
-
How many iterations before printing a new report? Encoded in log10.
- getAggregateReceiver() - Method in class ReporterAggregate
-
- getAggregateReceiver() - Method in class ConsoleAggregatedReporter
-
- getAggregateReceiver() - Method in class CSVReporterAggregated
-
- getAggregateReceiver() - Method in class Log4JReporter
-
- getAggregateReceiver() - Method in class MemoryUsageReporter
-
- getAggregateReceiver() - Method in class OptimizationStepLogReporter
-
- getAggregateReceiver() - Method in class TextFile
-
- getAggregateTriggerBank() - Method in class FeedbackBeginParameters
-
- getAll() - Method in class MarksWithEnergyBreakdown
-
Certain features are stored for every object, so that we can reference them in our
calculations for the 'all' component
- getAllCacheNames() - Method in class CacheTransferSourceCollection
-
- getAllKernelFactories() - Method in class KernelProposer
-
- getAllowsChildren() - Method in class ErrorNodeImpl
-
- getAngle() - Method in class OrientationAxisAngle
-
Angle part of axis-angle orientation (anti-clock in radians).
- getAngleDegrees() - Method in class Orientation2D
-
The angle of the rotation in the 2D plane anti-clockwise, in degrees.
- getAnnealScheme() - Method in class SimulatedAnnealing
-
- getAnnotations() - Method in class FromAnnotations
-
- getAnnotatorStrategy() - Method in class AnnotationInputManager
-
The strategy to be used for annotating.
- getAppendChannels() - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file somewhere else in the project's structure
- getAppendCSV() - Method in class FromCSVInputManager
-
- getAppendCsv() - Method in class MatchedAppendCsv
-
- getAppendDictionary() - Method in class MultiInputManager
-
- getAppendFilePath() - Method in class MultiInputManager
-
- getAppendHistogram() - Method in class MultiInputManager
-
- getAppendMarks() - Method in class MultiInputManager
-
- getAppendMarksFromAnnotation() - Method in class MultiInputManager
-
- getAppendMarksFromAnnotationAcceptedOnly() - Method in class MultiInputManager
-
- getAppendMarksFromAnnotationRejectedOnly() - Method in class MultiInputManager
-
- getAppendObjects() - Method in class MultiInputManager
-
- getAppendStack() - Method in class MultiInputManager
-
- getArbitraryElement() - Method in interface NamedProvider
-
Gets one element of the provider (arbitrarily).
- getArrange() - Method in class ArrangeRaster
-
- getArrange() - Method in class Cell
-
- getArrange() - Method in class CombineRasterGenerator
-
- getAsBoolean() - Method in interface CheckedBooleanSupplier
-
Applies a supplier like with BooleanSupplier.getAsBoolean().
- getAsDouble(String) - Method in class Dictionary
-
Retrieves a value from the dictionary, and converts to a double.
- getAssigner() - Method in class CompareAnnotations
-
- getAssignmentCSV() - Method in class ComparisonSharedState
-
- getAssignMode() - Method in class SimulatedAnnealing
-
- getAssociatedElementRange() - Method in class MutableDirectory
-
- getAssociatedElementRange() - Method in interface SequencedDirectory
-
The associated element-range with ths folder.
- getAssociatedMark() - Method in class ErrorNodeImpl
-
- getAsStack() - Method in class ChannelProvider
-
- getAsStack() - Method in class MaskProvider
-
- getAsStack() - Method in class StackProvider
-
- getAsStack() - Method in interface ProviderAsStack
-
Retrieves or creates a
Stack representation of an entity.
- getAsString(String) - Method in class Dictionary
-
Retrieves a value from the dictionary as a
String.
- getAttributes() - Method in class ImageTimestampsAttributes
-
Timestamps and other metadata associated with an image file-path, but not with the file's
contents.
- getAttributes() - Method in class StackWriteOptions
-
The attributes of the particular stack to write.
- getAxis() - Method in class AxisAlignedUnitVector
-
Which axis the unit-vector will align with.
- getAxis() - Method in class CenterOfGravity
-
- getAxis() - Method in class GradientForAxis
-
Which axis? X=0, Y=1, Z=2
- getAxis() - Method in class ForSpecificAxis
-
- getAxis() - Method in class ArbitraryInsidePoint
-
- getAxis() - Method in class BoundingBoxAlongAxisBase
-
- getAxis() - Method in class GradientMeanForAxis
-
- getAxis() - Method in class PrincipalAxisOrientation
-
Which axis to read from (x,y,z)
- getAxis() - Method in class BoundingBoxExtent
-
- getAxis() - Method in class OrientationAxisAngle
-
Axis part of axis-angle orientation (should be normalized).
- getAxisColor() - Method in class PlotColorScheme
-
- getAxisMax() - Method in class AxisLimits
-
- getAxisMin() - Method in class AxisLimits
-
- getBackground() - Method in class AnnotatorStrategy
-
The visual background to use while annotating.
- getBackground() - Method in class ObjectsAsRGBGenerator
-
A background image or dimensions to define an empty background.
- getBackground() - Method in class DualStack
-
The background
- getBackground() - Method in class CompareAnnotations
-
The name of the stack to use as background to the annotations.
- getBackground() - Method in class ColoredBase
-
The background.
- getBackgroundChannelIndex() - Method in class OutlinePreserveRelativeSize
-
Uses only this channel (identified by an index in the stack) as the background, -1 disables.
- getBackgroundChannelProvider() - Method in class MorphologicalOperatorBase
-
- getBackgroundColor() - Method in class PlotColorScheme
-
- getBackgroundID() - Method in class VisualizeOnBackground
-
- getBackgroundStackMap() - Method in class AnnotationBackground
-
If non-null, maps underlying stack-name to a background.
- getBackgroundStackName() - Method in class SegmentIntoMarks
-
- getBaseName() - Method in class FilenameSplitExtension
-
The part of the filename without an extension.
- getBeanExtension() - Method in class QuickMultiDatasetExperiment
-
- getBeanExtension() - Method in class QuickMultiDatasetStructuredExperiment
-
- getBeanName() - Method in class AnchorBean
-
A short-name identifying a bean (by default the name of the class associated with the bean).
- getBelowMinValue() - Method in class RangeCompareBase
-
Constant to return if outside the range (below the minimum allowed)
- getBest() - Method in class DualState
-
- getBest() - Method in class OptimizationStep
-
- getBestState() - Method in class Reporting
-
- getBinaryInputChannelID() - Method in class AddDistanceTransform
-
The ID of the binary input mask that determines the region of the Watershed.
- getBinarySgmn() - Method in class BinarySegmentByObject
-
- getBirthRepeats() - Method in class KernelReplace
-
- getBitDepthPerChannel() - Method in class ImageMetadata
-
The number of bits in memory to describe each voxel's intensity, per channel.
- getBitsPerPixel() - Method in class ForceBitsPerPixel
-
- getBlockSize() - Method in class HOGParameters
-
The block-size as per OpenCV implementation (identical default-size).
- getBlockStride() - Method in class HOGParameters
-
The block-stride as per OpenCV implementation (identical default-size).
- getBlue() - Method in class RGBColorBean
-
The blue component value of the RGB color.
- getBlue() - Method in class RGBColor
-
The blue component value of the RGB color.
- getBlue() - Method in class ThreeChannels
-
- getBorderWidth() - Method in class MontageSlices
-
Adds a border around each part of the montage
- getBoundRadius() - Method in class MarkWithPositionAndSingleRadius
-
- getBounds() - Method in class RandomOrientation
-
- getBridgeMatcher() - Method in class Bridge
-
Used to match each input-object to an intermediary-object
- getBundleSize() - Method in class ObjectSerializerPeriodicReporter
-
- getBundleSize() - Method in class VoxelizedMarksChangeReporter
-
- getCache() - Method in interface FeatureCalculationInput
-
- getCache() - Method in class CacheAndReuseStrategy
-
- getCache() - Method in class SessionInputSequential
-
- getCacheNames() - Method in class CacheTransferSource
-
- getCacheSize() - Method in class RelationWithMatches
-
Size of feature evaluation cache for featureEvaluatorMatch
- getCalculateLevel() - Method in class CalculateLevelOne
-
- getCalculateLevel() - Method in class ThresholderGlobal
-
- getCalculateLevel() - Method in class LevelPerObjectBase
-
Method to calculate the level for a particular object.
- getCalculateLevel() - Method in class GreaterThanThreshold
-
Calculates the level for the threshold
- getCalculateLevel() - Method in class LevelFromHistogram
-
- getCalculateLevel() - Method in class ThresholdHistogram
-
- getCalculateLevel() - Method in class CalculateLevelBase
-
- getCalculateLevelElse() - Method in class CalculateLevelRelativeToThreshold
-
- getCalculator() - Method in class NamedFeatureCalculatorMulti
-
- getCellDefault() - Method in class Tile
-
- getCells() - Method in class Tile
-
- getCellSize() - Method in class HOGParameters
-
The cell-size as per OpenCV implementation (identical default-size).
- getCenter() - Method in class SlidingBuffer
-
The buffer for the currently selected slice.
- getCenterPoint() - Method in class FitResult
-
- getCenterPointX() - Method in class EllipseStandardFormConverter
-
- getCenterPointY() - Method in class EllipseStandardFormConverter
-
- getChangedMarkIDArr() - Method in class KernelDecision
-
- getChangedMarkIDs() - Method in class Reporting
-
- getChannel(int) - Method in class EnergyStack
-
Returns the channel at a particular position in the stack.
- getChannel(int) - Method in class EnergyStackWithoutParameters
-
Returns the channel at a particular position in the stack.
- getChannel() - Method in class ChannelProviderUnary
-
- getChannel(int) - Method in class RGBStack
-
Returns the channel at a particular position in the stack.
- getChannel(int) - Method in class Stack
-
Returns the channel at a particular position in the stack.
- getChannel(int) - Method in class StackNotUniformSized
-
Returns the channel at a particular position in the stack.
- getChannel(String, int, Progress, Logger) - Method in class ChannelFilter
-
- getChannel() - Method in class ChannelFilter
-
- getChannel(String, int, Progress, Logger) - Method in interface ChannelGetter
-
- getChannel(String, int, Progress, Logger) - Method in class NamedChannelsForSeriesConcatenate
-
- getChannel(String, int, Progress, Logger) - Method in class NamedChannelsForSeriesMap
-
- getChannel() - Method in class FromChannel
-
- getChannel() - Method in class FromChannel
-
- getChannel() - Method in class FromChannelBase
-
- getChannel() - Method in class IntensityGreaterEqualThan
-
- getChannel() - Method in class UnaryWithChannelBase
-
- getChannel() - Method in class WithChannelBase
-
- getChannel() - Method in class FromChannelOrMask
-
A channel that is provided to the stack.
- getChannel() - Method in class NamedChannel
-
- getChannel(String, Logger) - Method in class ChannelGetterForTimepoint
-
- getChannel1() - Method in class ChannelProviderBinary
-
- getChannel1() - Method in class ChannelProviderTernary
-
- getChannel2() - Method in class ChannelProviderBinary
-
- getChannel2() - Method in class ChannelProviderTernary
-
- getChannel3() - Method in class ChannelProviderTernary
-
- getChannelAssignFrom() - Method in class AssignFromChannel
-
- getChannelChecker() - Method in class GroupedSharedState
-
- getChannelConversionStyle() - Method in class ConvertImageFormat
-
To convert as RGB or independently or in another way.
- getChannelConverter() - Method in class Convert
-
- getChannelConverter() - Method in class ConvertImageFormat
-
Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
- getChannelElse() - Method in class IfParamEquals
-
- getChannelFilter() - Method in class ConvertImageFormat
-
Optionally, includes only certain channels when converting.
- getChannelFirst() - Method in class Difference
-
Index of first channel
- getChannelGroupID() - Method in class RegularExpression
-
- getChannelID() - Method in class AddEdgeFilters
-
The ID of the channel that provides the input to the filter
- getChannelIfVoxelZero() - Method in class IfVoxelZero
-
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in
this channel instead
- getChannelIndex() - Method in class FromStack
-
- getChannelIndex() - Method in class FromStackChannel
-
- getChannelIndex() - Method in class One
-
- getChannelIndex() - Method in class FileDetails
-
- getChannelIndex() - Method in class MultiInputManagerQuick
-
If either stackAsChannel==true or we have specified additionalChannels this indicated which
channel to use from the stack
- getChannelLookup() - Method in class NormalizeDifferenceToMedian
-
- getChannelMap() - Method in class NamedChannels
-
- getChannelMask() - Method in class ExportImageHistograms
-
If defined, this is the name of channel used as a mask over the values which are fed into the
histogram
- getChannelName() - Method in class ChannelFilter
-
- getChannelName() - Method in class SingleChannel
-
- getChannelName() - Method in class ConvertNamedChannelsToStack
-
By default all channels are converted into a stack.
- getChannelNum() - Method in class SortedSetChannel
-
- getChannelOptional(String, int, Progress, Logger) - Method in interface NamedChannelsForSeries
-
Gets a channel if it exists, returning empty if it doesn't.
- getChannelOptional(String, int, Progress, Logger) - Method in class NamedChannelsForSeriesConcatenate
-
- getChannelOptional(String, int, Progress, Logger) - Method in class NamedChannelsForSeriesMap
-
- getChannelSecond() - Method in class Difference
-
Index of second channel
- getChannelsExtra() - Method in class ScoreVoxels
-
- getChannelsPerByteArray() - Method in class ForceChannelsPerByteArray
-
- getChannelThreshold() - Method in class ThresholdAgainstChannel
-
- getChannelType() - Method in class ConsistentChannelChecker
-
- getChart() - Method in class PlotInstance
-
- getCheck() - Method in class Not
-
- getChecked() - Method in class Outputter
-
- getCheckMark() - Method in class FromObjects
-
- getCheckMark() - Method in class Check
-
- getCheckMark() - Method in class Check
-
- getCheckParsedFilePathBag() - Method in class GroupFiles
-
Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be
included.
- getChildAt(int) - Method in class ErrorNodeImpl
-
- getChildCount() - Method in class ErrorNodeImpl
-
- getClassifierProvider() - Method in class BinaryClassifierImageLabeller
-
- getCode(int) - Method in class EncodedIntBuffer
-
- getCol(int) - Method in class TableItemArrangement
-
- getCol() - Method in class Cell
-
- getColForListIndex(int) - Method in class TableItemArrangement
-
- getCollection() - Method in class KernelDeath.MarkAnd
-
- getColor() - Method in class FromSingle
-
The single color to repeat.
- getColor(int) - Method in class ColoredOverlayCollection
-
- getColor() - Method in class AnnotationLabel
-
An optional color associated with the label when displayed via GUI
- getColor() - Method in class ColoredMask
-
- getColorIDGetter() - Method in class ObjectDrawAttributes
-
Gets a color ID associated with the object
- getColorIndex() - Method in class ObjectDrawAttributes
-
Colors for a given index
- getColorList() - Method in class ColoredMarks
-
- getColors() - Method in class ColorSchemeUnary
-
The delegate that creates the color-list before subsequent processing.
- getColors() - Method in class FromList
-
The list of colors to specify.
- getColors() - Method in class ColoredOverlayCollection
-
- getColors() - Method in class ColoredBaseWithGenerator
-
Colors to use for drawing objects
- getColors() - Method in class ColoredObjectCollection
-
The colors in the collection.
- getColorScheme() - Method in class GenerateToMatchObjects
-
- getColorsUnpaired() - Method in class CompareAnnotations
-
- getColorUnselectedObjects() - Method in class OutlinePreserveRelativeSize
-
Optionally outline the other (unselected for the thumbnail) objects in this particular color.
- getColumnDefinition() - Method in class ExportObjectsFromCSV
-
Column definition for the CSV files
- getColumnGroup() - Method in class ColumnDefinition
-
Name of CSV column used to group results (the same values, are outputted together)
- getColumnID() - Method in class ColumnDefinition
-
Name of CSV column with the file identifier
- getColumns() - Method in class MontageSlices
-
How many columns to use in the montage, or 0 to guess an approximately square output
- getColumnUniquePixel() - Method in class ColumnDefinition
-
Name of CSV column with X coordinate of point for the first Object
- getCombine() - Method in class FromObjects
-
- getCombined() - Method in interface VoxelPartition
-
- getCombined() - Method in class VoxelPartitionHistogram
-
- getCommand() - Method in class MorphologicalOperation
-
One of: open, close, fill, erode, dilate, skel, outline
- getCommandName() - Method in class HelpConfig
-
What the application command is described as in the help message e.g. anchor or
anchorGUI
- getComparerLeft() - Method in class AnnotationComparisonInputManager
-
- getComparerMultiplex(boolean) - Method in class AnnotationComparisonInput
-
- getComparerRight() - Method in class AnnotationComparisonInputManager
-
- getComparers() - Method in class AnnotationComparisonInput
-
- getCondition() - Method in class IfParamEquals
-
- getCondition() - Method in class IfKeyValueCondition
-
- getConnPoint() - Method in class ContiguousVoxelPath
-
- getConstant() - Method in class MaxWithConstant
-
- getContains() - Method in class DescriptiveNameContainsImageLabeller
-
- getContains() - Method in class FilterDescriptiveName
-
A descriptive-name must contain (case-sensitive) this string.
- getContext() - Method in class SharedObjects
-
Logger and other common configuration
- getContext() - Method in class ParametersExperiment
-
- getContext() - Method in class OutputterChecked
-
General settings for writing outputs.
- getContext() - Method in class FeatureCalculationContext
-
- getContext() - Method in class FeatureExporterContext
-
Context for reading from or writing outputs to the file-system.
- getContextExperiment() - Method in class InputBound
-
The input-output context associated with the current experiment.
- getContextJob() - Method in class InputBound
-
The input-output context associated with the current job.
- getConversion() - Method in class ConvertedInput
-
The converted input.
- getConvert() - Method in class ConvertWithHistogram
-
- getConverters() - Method in class DisplayStack
-
A list of optional converters that will be applied to the respective channel in stack
if they exist.
- getCopyFilesNaming() - Method in class CopyFilesNamingOne
-
- getCost(int, int) - Method in class CostMatrix
-
Gets the cost from an element from the first-list to an element from the second-list.
- getCost() - Method in class MergeStrategy
-
A cost of how undesirable (the higher the more undesirable) this merge is.
- getCosts() - Method in class AssignOverlappingObjects
-
A matrix linking the overlap between each
ObjectMask to each other, respectively as
rows and columns.
- getCount() - Method in class RecordedExecutionTimes.RecordedOperation
-
How many times the operation occurred.
- getCount() - Method in class Counter
-
The count, as per current state.
- getCount() - Method in class RunningSum
-
The running count.
- getCount(int) - Method in class Histogram
-
The count corresponding to a particular value.
- getCount() - Method in class VarianceCalculatorDouble
-
The running count of values.
- getCount() - Method in class VarianceCalculatorLong
-
The running count of values.
- getCountThreshold() - Method in class SummarizerSplitMoreThan
-
If there are more than countThreshold elements, use summarizerGreaterThan,
else summarizerElse.
- getCreateMark() - Method in class PointsFitter
-
- getCreationTime() - Method in class ImageFileAttributes
-
The creation timestamp on the file the image was loaded from.
- getCsvFeaturesAggregated() - Method in class FeatureOutputNames
-
The CSV of aggregated feature-results, if enabled.
- getCsvFeaturesGroup() - Method in class FeatureOutputNames
-
The CSV individually written for each group, if enabled.
- getCsvFeaturesNonAggregated() - Method in class FeatureOutputNames
-
The CSV of non-aggregated feature-results.
- getCsvFilePath() - Method in class FilterCSVColumn
-
- getCsvFilePath() - Method in class FromCSVInput
-
- getCurrent() - Method in class DualState
-
- getCurrent() - Method in class OptimizationStep
-
- getCurrentTemp() - Method in class Geometry
-
- getCustomName() - Method in class Feature
-
An optional additional name that be associated with the feature (defaults to an empty
string).
- getDatasetName() - Method in class ExperimentResultsExperimentStructure
-
The name of the experiment including version suffix
- getDatasets() - Method in class QuickMultiDatasetExperiment
-
- getDatasets() - Method in class QuickMultiDatasetStructuredExperiment
-
- getDatasetSpecific() - Method in class QuickMultiDatasetExperiment
-
- getDatasetSpecific() - Method in class QuickMultiDatasetStructuredExperiment
-
- getDatasetSuffix() - Method in class FilePathAppendBase
-
A suffix appended to the dataset name extracted from the reg exp
- getDatasetVersion() - Method in class ExperimentResultsExperimentStructure
-
A version-suffix appended to the dataset name extracted from the reg exp
- getDebugModeParameters() - Method in class InputManagerParameters
-
- getDebugModeParameters() - Method in class InputContextParameters
-
Parameters for debug-mode (only defined if we are in debug mode)
- getDefault() - Static method in class BinaryValuesByte
-
Default values to use, if not otherwise specified.
- getDefault() - Static method in class BinaryValuesInt
-
Default values to use, if not otherwise specified.
- getDefaultBeanClass() - Method in class AnchorDefaultBeanFactory
-
Returns null as
Optional is not supported by
BeanFactory interface.
- getDefaultColors() - Method in class OutputWriteSettings
-
The default color-scheme used for outputs, if no other scheme is specified.
- getDefaultExtension() - Method in interface FileFormat
-
The default extension to write associated with a particular format.
- getDefaultExtension() - Method in enum ImageFileFormat
-
- getDefaultExtension() - Method in enum NonImageFileFormat
-
- getDefaultInstances() - Method in class AnchorDefaultBeanFactory
-
Default bean-classes to use for particular family types of beans.
- getDefaultInstances() - Static method in class RegisterBeanFactories
-
Default instances of different family-types of beans.
- getDefaultStackReaderForMetadata() - Method in class ConvertNamedChannels
-
Supplies to the imageMetadataReader to use, if no other reader is specified.
- getDefine() - Method in class MarkEvaluator
-
- getDefine() - Method in class DefineOutputter
-
- getDefine() - Method in class Develop
-
Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
- getDefine() - Method in class ExportReportFeaturesFromMulti
-
- getDefine() - Method in class FromObjects
-
- getDefine() - Method in class ExportObjectsAsCroppedImages
-
- getDefine() - Method in class SegmentWithMarkedPointProcess
-
Adds definitions of stacks/objects etc.
- getDelaySizeAtEnd() - Method in class MovieFromSlices
-
- getDelegate() - Method in class RasterGeneratorDelegateToRaster
-
- getDelegate() - Method in class UnsignedByteBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class UnsignedIntBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class UnsignedShortBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class InputFromManagerDelegate
-
- getDelegate() - Method in class BoundMinMax
-
- getDelegate() - Method in class CalculateInputFromDelegate
-
- getDelimiter() - Method in class SubsetRangeIfRequested
-
Character used to split the name into groups.
- getDelimiter() - Method in class LastDirectoryAsPrefix
-
- getDelta() - Method in class Mser
-
- getDeltat() - Method in class AnisotropicDiffusion
-
the integration constant for the numerical integration scheme.
- getDepth() - Method in class TraversalResult
-
The depth of directories processed, where 1 = root directory traversed, 2 = root directory +
one further level etc.
- getDepth() - Method in class ImposeResolution
-
Physical pixel size of a voxel in z-dimension.
- getDerivePath() - Method in class DualMarksAnnotationAsObjects
-
- getDerivePath() - Method in class MarksAsObjects
-
- getDerivePath() - Method in class MaskAsObject
-
Where to find the
Mask to compare, as a function of the source file-path.
- getDerivePath() - Method in class Objects
-
Where to find the objects to compare, as a function of the source file-path.
- getDerivePath() - Method in class CollapseFileName
-
- getDerivePath() - Method in class RemoveTrailingDirectory
-
- getDescription() - Method in exception AnchorCombinableException
-
The (uncombined) description associated with the exception.
- getDescription() - Method in class OutputtedFile
-
- getDescription() - Method in class ManifestDirectoryDescription
-
- getDescription() - Method in class KernelDecision
-
- getDescription() - Method in class KernelWithIdentifier
-
- getDestination() - Method in class IdentifiablePair
-
- getDestination() - Method in class PairPxlMarkMemo
-
- getDestination() - Method in class DualVoxelizedMarks
-
- getDestination() - Method in class ToVoxelized
-
- getDestinationDirectory() - Method in class CopyContext
-
Destination directory for copying.
- getDictionaries() - Method in class DictionaryInitialization
-
- getDictionary() - Method in class FeatureInitialization
-
A dictionary of key-value pairs.
- getDictionary() - Method in class FeatureRelatedInitialization
-
- getDictionary() - Method in class FeatureEvaluator
-
Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
- getDictionary() - Method in class EnergySchemeCreatorByElement
-
- getDictionary() - Method in class ScaleByDictionary
-
- getDictionary() - Method in class AssignFromDictionary
-
The dictionary from which an assignment will occur.
- getDictionary() - Method in class ScoreVoxels
-
- getDictionary() - Method in class DictionaryCondition
-
The dictionary to provide a value to check.
- getDictionary() - Method in class IfParamEqual
-
- getDictionary() - Method in class ParamFromCollection
-
- getDictionary() - Method in class FeatureListProviderLDAClassifier
-
- getDictionary() - Method in class FeatureValueCheckMark
-
- getDictionary() - Method in class DefineOutputterWithEnergy
-
- getDictionary() - Method in class GaussianSampler
-
The dictionary that parameterizes the Gaussian-distribution that is sampled from.
- getDictionary() - Method in class Develop
-
If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
- getDictionary() - Method in class SegmentMarksFromImage
-
If non-empty, a dictionary that is passed to the segmentation procedure.
- getDictionaryOptional() - Method in interface FeatureInputDictionary
-
The associated dictionary, if it exists.
- getDictionaryOptional() - Method in class FeatureInputEnergy
-
- getDictionaryOptional() - Method in class FeatureInputMark
-
- getDictionaryRequired() - Method in interface FeatureInputDictionary
-
The associated dictionary, or an exception if it doesn't exist.
- getDimensions() - Method in class ImageMetadata
-
The dimensions of the image.
- getDimensions() - Method in class ReportFeatureForMarks
-
- getDimensions() - Method in class FromDimensionsBase
-
- getDimensions() - Method in class FromDimensionsBase
-
- getDimensions() - Method in class RepeatSlice
-
Dimensions to create new mask
- getDimensions() - Method in class MergeBase
-
- getDimensions() - Method in class WithDimensionsBase
-
- getDimensions() - Method in class WithOptionalDimensionsBase
-
- getDimensions() - Method in class ToDimensions
-
The dimensions the source image/entity is desired to be scaled to.
- getDimensions() - Method in class FromMarks
-
- getDimensions() - Method in class RequireFeatureRelationThreshold
-
- getDimensions() - Method in class PointsFitterToMark
-
- getDimensionsOptional() - Method in class FeatureInputMark
-
- getDimensionsRequired() - Method in class FeatureInputMark
-
- getDimensionsSourceFallback() - Method in class ToDimensions
-
- getDirection() - Method in class ConvertToPhysicalDistance
-
Direction of the distance being converted, defaults to a unit vector along the X-axis
- getDirection() - Method in class FeatureMarkDirection
-
- getDirectionVector() - Method in class LineSegment
-
- getDirectionVector() - Method in class FromUnitValueDistance
-
- getDirectory() - Method in class PathDifference
-
The directory component of the difference, if it exists.
- getDirectory() - Method in class InputArguments
-
A directory indicating where inputs can be located
- getDirectory() - Method in class FilesProviderWithDirectoryString
-
A directory in which to look for files.
- getDirectory() - Method in class FileWithDirectoryInput
-
A directory that must be a containing directory (at some hierarchical level) of file
associated with this input.
- getDirectory() - Method in class GlobExtractor.GlobWithDirectory
-
The directory part of the string, or null if it doesn't exist
- getDirectory() - Method in class DualPathPredicates
-
Only accepts any containing directories where the predicate returns true
- getDirectory() - Method in class OutputterTarget
-
- getDirectory() - Method in class DirectoryWithPrefix
-
- getDirectory() - Method in class HomeSubdirectory
-
A relative-path (to the user home directory) which is used as an output directory
- getDirectoryAsPath(InputContextParameters) - Method in class FilesProviderWithDirectory
-
- getDirectoryAsPath(InputContextParameters) - Method in class FilesProviderWithDirectoryString
-
- getDirectoryAsPath(InputContextParameters) - Method in class FilesProviderWithDirectoryUnary
-
- getDirectoryAsPath(InputContextParameters) - Method in class SingleFile
-
- getDirectoryAsPathEnsureAbsolute(InputContextParameters) - Method in class FilesProviderWithDirectory
-
Like getDirectory as Path but converts any relative path to absolute one
- getDirectoryDataset() - Method in class QuickMultiDatasetExperiment
-
- getDirectoryDistance() - Method in class QuickMultiDatasetStructuredExperiment
-
How many directories to recurse back from the current file to the Experiments/ directory
- getDirectoryOutput() - Method in class QuickExperiment
-
- getDistance() - Method in class LevelPerObjectNeighbors
-
How many neighbors to include by distance (distance==1 implies all directly touching
neighbors, distance==2 implies those touching the directly touching etc.)
- getDistance() - Method in class DistanceIndex
-
- getDistance() - Method in class DistanceIndexTwice
-
- getDistanceMapProvider() - Method in class MergeSpatialClusters
-
A distance map which can also be used for making decisions on merging
- getDistanceMax() - Method in class CalculateLevel
-
- getDistanceTransformMultiplyBy() - Method in class AddDistanceTransform
-
Multiplies the distance transform by this factor to make it more meaningful in a short.
- getDistanceTransformSmoothSigmaMeters() - Method in class AddDistanceTransform
-
If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters
below.
- getDistanceX() - Method in class ReflectInAxesWithinDistance
-
- getDistanceY() - Method in class ReflectInAxesWithinDistance
-
- getDistanceZ() - Method in class ReflectInAxesWithinDistance
-
- getDistanceZEndIfEmpty() - Method in class XYOrientationExtendToZ
-
- getDivideByZeroValue() - Method in class Divide
-
- getDivisor() - Method in class PermutePropertySequenceDouble
-
What to divide the integer-sequence by.
- getDrawObject() - Method in class SimpleOverlayWriter
-
- getDrawObject() - Method in class DrawOverlay
-
- getDscr() - Method in class ResolvedBound
-
- getDualStack() - Method in class OptimizationContext
-
- getEigenvalue() - Method in class EigenvalueAndVector
-
The eigenvalue.
- getEigenvector() - Method in class EigenvalueAndVector
-
The eigenvector corresponding to eigenvalue.
- getElemAllAsFeatureList() - Method in class EnergyScheme
-
- getElemAllCreator() - Method in class EnergySchemeCreatorByElement
-
- getElemByCliqueSize(int) - Method in class EnergyScheme
-
- getElemIndAsFeatureList() - Method in class EnergyScheme
-
- getElemIndCreator() - Method in class EnergySchemeCreatorByElement
-
- getElemPairAsFeatureList() - Method in class EnergyScheme
-
- getElemPairCreator() - Method in class EnergySchemeCreatorByElement
-
- getEllipsoidCalculator() - Method in class Ellipsoid
-
- getEllipsoidSum(double, double, double, DoubleMatrix2D) - Static method in class Ellipsoid
-
- getElseName() - Method in class FileNamerContext
-
A fallback name, if a failure occurs when naming.
- getEmptyValue() - Method in class CenterOfGravity
-
- getEmptyValue() - Method in class Intersection
-
- getEmptyValue() - Method in class ArbitraryInsidePoint
-
- getEmptyValue() - Method in class IntensityMeanMaxSlice
-
- getEmptyValue() - Method in class IntensityMeanShellBase
-
- getEmptyValue() - Method in class DerivedObject
-
- getEnd() - Method in class SequenceInteger
-
An index beyond which we cannot iterate (inclusive).
- getEndIndex() - Method in class IndexRangeNegative
-
The index if the last element to use in the subsetting range, inclusive.
- getEndPoint() - Method in class LineSegment
-
- getEnergy() - Method in class Aggregator
-
- getEnergyChannelIndex() - Method in class Identity
-
- getEnergyChannelIndex() - Method in class RejectIfIntensityLessThan
-
- getEnergyChannelIndex() - Method in class SingleChannel
-
- getEnergyChannelIndex() - Method in class QuantileAcrossConnectedComponents
-
- getEnergyChannelIndexCheck() - Method in class IdentityImposeValueRelationToHistogram
-
- getEnergyChannelIndexFail() - Method in class IdentityImposeValueRelationToHistogram
-
- getEnergyIndex() - Method in class NumberNeighboringVoxels
-
Index of which channel in the energy-stack to select
- getEnergyIndex() - Method in class SpecificEnergyChannelBase
-
Index of which channel in the energy-stack to select
- getEnergyIndex() - Method in class FeatureEnergyChannel
-
Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
- getEnergyIndex() - Method in class OutsideRange
-
- getEnergyIndex() - Method in class Intensity
-
The channel that that forms the histogram
- getEnergyIndex() - Method in class AsObjectMask
-
The channel that that forms an object-mask with the bounding-box set to entire channel's
dimensions
- getEnergyIndex() - Method in class OverlapMaskBase
-
- getEnergyIndexGradient() - Method in class TextureScore
-
- getEnergyIndexMask() - Method in class IntensityMeanShellBase
-
A channel of the energyStack that is used as an additional mask using default byte values for
on and off.
- getEnergyIndexMask() - Method in class Intensity
-
Optionally, index of another channel that masks the histogram.
- getEnergyIndexX() - Method in class IntensityGradientBase
-
- getEnergyIndexY() - Method in class IntensityGradientBase
-
- getEnergyIndexZ() - Method in class IntensityGradientBase
-
- getEnergyScheme() - Method in class MarksWithEnergyBreakdown
-
- getEnergyScheme() - Method in class MarksWithTotalEnergy
-
Associated Energy Scheme, which should include the EnergySavedPairs
- getEnergyScheme() - Method in class VoxelizedMarksWithEnergy
-
- getEnergyScheme() - Method in class EnergySchemeWithSharedFeatures
-
- getEnergyScheme() - Method in class KernelCalculationContext
-
- getEnergyScheme() - Method in class OptimizationContext
-
- getEnergySchemeCreator() - Method in class MarkEvaluator
-
- getEnergySchemeCreator() - Method in class SegmentWithMarkedPointProcess
-
Creates an energy scheme that assigns an energy score to each collection of marks.
- getEnergyStack() - Method in class FeatureInitialization
-
An energy-stack, which may form an input to the feature for calculation.
- getEnergyStack() - Method in class ProposerContext
-
- getEnergyStack() - Method in class DualStack
-
The energy-stack
- getEnergyStack() - Method in class FeatureCalculatorFromProvider
-
- getEnergyStack() - Method in class InitializationWithEnergyStack
-
- getEnergyStackOptional() - Method in class FeatureInputEnergy
-
The associated energy-stack.
- getEnergyStackRequired() - Method in class FeatureInputEnergy
-
The associated energy-stack or throws an exception if it isn't present.
- getEnergyTotal() - Method in class EnergyPair
-
- getEnergyTotal() - Method in class MarksWithEnergyBreakdown
-
- getEnergyTotal() - Method in class MarksWithTotalEnergy
-
The pre-annealed total energy
- getEnergyTotal() - Method in class VoxelizedMarksWithEnergy
-
- getEnergyTotal() - Method in class EnergySavedAll
-
- getEnergyTotal() - Method in class EnergySavedInd
-
- getEnergyTotal() - Method in class EnergySavedPairs
-
Pairwise energy total
- getEquals() - Method in class FilterDescriptiveName
-
A descriptive-name must be exactly equal to (case-sensitive) this string.
- getError(int) - Method in class ResultsVector
-
Gets an error state at a particular position.
- getErrorMessage() - Method in class ErrorNodeImpl
-
- getErrorNode() - Method in class ProposerContext
-
- getErrorReporter() - Method in interface InputOutputContext
-
The associated error reporter.
- getErrorReporter() - Method in class Outputter
-
- getErrorReporter() - Method in class GraphLogger
-
- getErrorTree() - Method in class ProposerFailureDescription
-
- getExactDepth() - Method in class DirectoryDepth
-
- getException() - Method in exception CheckedStream.ConvertedToRuntimeException
-
- getException(String) - Method in interface NamedProvider
-
Retrieves the item if it exists, or throws an exception if it doesn't exist.
- getException(String) - Method in class LazyEvaluationStore
-
- getException(String) - Method in class SharedFeaturesSubset
-
Gets a feature by name, throwing an exception if it doesn't exist.
- getException(String) - Method in class NamedEntries
-
- getExecutionTime() - Method in class KernelDecision
-
- getExecutionTime() - Method in class Reporting
-
- getExecutionTimeRecorder() - Method in class ExperimentFeedbackContext
-
Allows execution-time for particular operations to be recorded.
- getExecutionTimeRecorder() - Method in class InputOutputContextStateful
-
- getExecutionTimeRecorder() - Method in class ParametersExperiment
-
Allows execution-time for particular operations to be recorded.
- getExecutionTimeRecorder() - Method in class InputManagerParameters
-
Allows for recording the execution-time of particular operations.
- getExecutionTimeRecorder() - Method in interface InputOutputContext
-
Allows execution-times to be recorded for particular operations.
- getExecutionTimeRecorder() - Method in class OutputWriteContext
-
Records the execution time of particular operations.
- getExecutionTimeRecorder() - Method in class ElementOutputter
-
Records the execution time of particular operations.
- getExecutionTimeRecorder() - Method in class FeatureCalculationContext
-
Records the execution-time of particular operations.
- getExperiment() - Method in class ExperimentResultsExperimentStructure
-
- getExperiment() - Method in class ExperimentStructure
-
- getExperimentalManifest() - Method in class ParametersExperiment
-
- getExperimentArguments() - Method in class InputOutputContextStateful
-
- getExperimentArguments() - Method in class ParametersExperiment
-
- getExperimentDescription() - Method in class OptimizationContext
-
- getExperimentIdentifier() - Method in class OutputExperiment
-
A name for the experiment.
- getExperimentIdentifier() - Method in class ParametersExperiment
-
- getExperimentManifest() - Method in class CoupledManifests
-
- getExperimentType() - Method in class FilePathAppendBase
-
A folder identifying the type of experiment (where the outputs are all put in the same
directory
- getExperimentType() - Method in class QuickMultiDatasetStructuredExperiment
-
The value of $1 (see comment above) in naming-structure.
- getExperimentType() - Method in class RootedExperiment
-
A directory identifying the type of experiment.
- getExpression() - Method in class RegExSimple
-
A Java-style regular expression containing groups.
- getExpression() - Method in class MatchRegularExpression
-
- getExpression() - Method in class RegularExpression
-
- getExtension() - Method in class FilenameSplitExtension
-
The extension of the filename.
- getExtension() - Method in class OneOrThreeChannelsWriter
-
- getExtension() - Method in class AppendStack
-
- getExtension() - Method in class AppendStackDirect
-
- getExtensions() - Method in class MatchExtensions
-
A set of file-extensions (without the period), one of which must match the end of a path.
- getExtensions() - Method in class BranchExtension
-
Any extensions to match (case insensitive) not including any leading period.
- getExtent() - Method in class KernelPointCursor
-
The size of the image the kernel iterates over.
- getExtractScoreSize() - Method in class DirectAssignMode
-
- getExtractScoreSize() - Method in class UniformProposal
-
- getExtractScoreSizeReport() - Method in class TransformationAssignMode
-
- getExtractScoreSizeState() - Method in class TransformationAssignMode
-
- getExtractWeight() - Method in class KernelInitialMarksFromPartition
-
- getExtraLength() - Method in class Midpoint
-
- getFactor() - Method in class ScoreObjects
-
- getFactor() - Method in class Scale
-
- getFactorHigh() - Method in class Identity
-
- getFactorLow() - Method in class Identity
-
- getFactorStandardDeviation() - Method in class GaussianSampler
-
Multiples the standard deviation of the distribution found in keyStandardDeviation.
- getFallback() - Method in class SpecificPathList
-
If no paths can be found either from listPaths or the input-context, then the fallback is
called if exists, otherwise an error is thrown
- getFallback() - Method in class ToSuggested
-
- getFallback() - Method in class RGB
-
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
- getFallback() - Method in class InferFromHeader
-
Fallback to use if EXIF information is non-existing or absent.
- getFallbackName() - Method in class ExperimentIdentifierAuto
-
If there's no task-name, then this constant is used as a fallback name
- getFeature() - Method in class FeatureProviderDefine
-
The feature to provide.
- getFeature() - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session.
- getFeature() - Method in class OutputFeatureTable
-
A list of features to calculate in an evaluation context.
- getFeature() - Method in class ScoreObjects
-
Feature that calculates the score for an object.
- getFeature() - Method in class PermuteFeatureBase
-
- getFeature() - Method in class AddCriteriaFeatureRelationThreshold
-
- getFeature() - Method in class FeatureValueCheckMark
-
- getFeature() - Method in class RequireFeatureRelationThreshold
-
- getFeatureCondition() - Method in class IfCondition
-
- getFeatureCondition() - Method in class IfConditionWithinRange
-
Calculates value for the condition - which is checked if it lies within a certain range
- getFeatureElse() - Method in class IfCondition
-
- getFeatureEvaluator() - Method in class MultipleComparer
-
Calculates the cost used when making assignments.
- getFeatureEvaluator() - Method in class ReportFeatureEvaluator
-
- getFeatureEvaluator() - Method in class FeatureCostAssigner
-
- getFeatureEvaluator() - Method in class DiscardOutliers
-
- getFeatureEvaluator() - Method in class RelationWithMatches
-
- getFeatureEvaluator() - Method in class ThresholdedFeature
-
- getFeatureEvaluator() - Method in class ObjectCollectionProviderWithFeature
-
- getFeatureEvaluator() - Method in class MergeGreedyToIncreaseObjectFeature
-
- getFeatureEvaluator() - Method in class MergeToIncreaseObjectFeature
-
- getFeatureEvaluatorMatch() - Method in class RelationWithMatches
-
- getFeatureEvaluatorMerge() - Method in class MergePairs
-
- getFeatureEvaluatorThreshold() - Method in class MergePairs
-
Allows merge only if the feature-value satisfies a relation to this threshold
- getFeatureLists() - Method in class FeatureRelatedInitialization
-
- getFeatureNameIndex() - Method in class FeatureInputResults
-
A mapping from the name of the feature that produced a result, to its index position in
results.
- getFeatureNames() - Method in class FeatureCalculationContext
-
The name of each feature being calculated, in identical order, as that is placed in the
exported CSV.
- getFeatureNames() - Method in class FeatureExporter
-
The names of the features to be exported.
- getFeatureProvider() - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session
- getFeatures() - Method in class FeatureListEvaluator
-
A list of providers, combined together to form a list of features, to be calculated in a
session
- getFeatures() - Method in class ExportFeatures
-
The features to be exported (after possibly some manipulation or augmentation).
- getFeatures() - Method in class SegmentInstanceWithModel
-
Features to calculate for objects in the features output.
- getFeaturesAggregate() - Method in class ExportFeatures
-
- getFeaturesImage() - Method in class PairNeighbors
-
Additional features that only depend on the image, so do not need to be replicated for every
object.
- getFeatureSource() - Method in class FeatureCalculationContext
-
The features that are calculated, encapsulated in some object.
- getFeaturesPair() - Method in class PairNeighbors
-
Additional features that are processed on the pair of images (i.e.
- getFeatureTables() - Method in class Develop
-
Specifies a feature-table that can also be outputted.
- getFeedbackReceiver() - Method in class FeedbackReceiverRequireArguments
-
- getFeedbackReceiver() - Method in class SegmentWithMarkedPointProcess
-
Processes feedback from the segmentation algorithm for outputting / debugging.
- getFile() - Method in class NamedChannelsInputPart
-
- getFile() - Method in class NamedFile
-
The file.
- getFile() - Method in class SingleFileInputBase
-
- getFile() - Method in class DualPathPredicates
-
Only accepts files where the predicate returns true
- getFileAttributes() - Method in class ImageMetadata
-
Attributes associated with the file on the filesystem.
- getFileExtension() - Method in class FileType
-
- getFileFilter() - Method in class ExperimentResultsExperimentStructure
-
Files to search for
- getFileId() - Method in class AppendCsv
-
Unique identifier for the stack, object-mask-collection etc.
- getFileId() - Method in class FilePathBaseAppendToManagerWithFileID
-
Unique identifier for the stack, object-mask-collection etc.
- getFileInput() - Method in class GroupFiles
-
- getFileInput() - Method in class NamedChannels
-
- getFileInput() - Method in class Stacks
-
- getFileInput() - Method in class QuickExperiment
-
A string indicating the input file(s)
- getFilename() - Method in class PathDifference
-
The file-name component of the difference, if it exists.
- getFileName() - Method in class OutputtedFile
-
- getFileName() - Method in class ReportFeatureForManifestFileBase
-
- getFilePath() - Method in class SortedSetSlice
-
- getFilePath() - Method in class FromSerializedMarks
-
- getFilePath() - Method in class FromSerializedObject
-
- getFilePathParser() - Method in class MultiFileReader
-
- getFilePathProviderSVM() - Method in class FeatureListProviderSVMClassifier
-
- getFilePaths() - Method in class FilePathInitialization
-
Named-store of file-paths.
- getFilePaths() - Method in class FeatureRelatedInitialization
-
A named-set of file-paths.
- getFilePrefix() - Method in class MovieFromSlices
-
- getFiles() - Method in class TraversalResult
-
All files in any directories that have been traversed.
- getFiles() - Method in class ReadFromFile
-
Provides a single file containing a dictionary.
- getFiles() - Method in class FilesProviderUnary
-
- getFiles() - Method in class FilesProviderWithDirectoryUnary
-
- getFiles() - Method in class FromFiles
-
A provider that should return exactly one
File whose path is employed.
- getFiles() - Method in class Rooted
-
- getFiles() - Method in class NamedFiles
-
The files to use as inputs.
- getFiles() - Method in class NamedFilesWithDirectory
-
The files to use as inputs.
- getFiles() - Method in class QuickBase
-
A path to the main channel of each file
- getFilter() - Method in class IfObjectFilter
-
- getFilter() - Method in class ObjectCollectionProviderFilterBase
-
- getFilter() - Method in class Filter
-
- getFilter() - Method in class ImageLabellerStringMap
-
- getFilterExtensions() - Method in class InputArguments
-
If defined, a set of extension filters that can be applied on inputDirectory
- getFilterFilesCsv() - Method in class QuickBase
-
If set, a CSV is read with two columns: the names of images and a
- getFilterGlob() - Method in class InputArguments
-
If defined, a glob that is applied on inputDirectory
- getFilterInitialization(Path) - Method in class SharedStateFilteredImageOutput
-
- getFindOutlinePixelAngle() - Method in class TraversePointsOnContour
-
- getFirst() - Method in class CostMatrix
-
The first set of elements.
- getFirst() - Method in class FeatureInputPairObjects
-
- getFirst() - Method in class OutputEnableRulesSpecify
-
Output-names in the first-level.
- getFirst() - Method in class Compose
-
First transformation from S to U
- getFirst() - Method in class PrecalculationOverlay
-
- getFirstArgument() - Method in class HelpConfig
-
What the application argument is described as in the help message
e.g. experimentFile.xml
- getFirstBinaryValues() - Method in class ObjectCollection
-
- getFirstBinaryValuesByte() - Method in class ObjectCollection
-
- getFloat() - Static method in class VoxelsFactory
-
A factory that creates voxels of type float.
- getFontColor() - Method in class TextStyle
-
Font-color of drawn text
- getFontName() - Method in class TextStyle
-
Font-name of drawn text
- getFontSize() - Method in class TextStyle
-
Font-size of drawn text
- getForAllSlices(int) - Method in class IndexByRegion
-
- getForceReader() - Method in class BioformatsReader
-
If non-empty forces usage of a particular bioformats plugin.
- getFormats() - Method in class InferFromHeader
-
The formats whose headers will be searched, to find sufficient metadata to populate
ImageMetadata.
- GetForSeries<T,S> - Interface in org.anchoranalysis.plot
-
- getForSlice(int, int) - Method in class IndexByRegion
-
- getFoundDirectory() - Method in class FinderSingleDirectory
-
- getFoundFile() - Method in class FinderSingleFile
-
- getFriendlyName() - Method in class Feature
-
A user-friendly human-readable name for the
Feature.
- getFrom() - Method in class TypedEdge
-
The vertex the edge joins from.
- getFunction() - Method in class ManifestDescription
-
Identifies the function the entity plays.
- getGaussianSigmaMeters() - Method in class AddEdgeFilters
-
- getGenerator() - Method in class BoundOutputter
-
The generator to be (repeatedly) used to write elements in the sequence.
- getGeneratorList() - Method in class CombineRasterGenerator
-
- getGlob() - Method in class MatchGlob
-
The string describing a glob e.g.
- getGlob() - Method in class GlobExtractor.GlobWithDirectory
-
- getGradient() - Method in class ScoreVoxels
-
- getGraphColorScheme() - Method in class PlotIndexBase
-
- getGrayscaleReconstruction() - Method in class MinimaImpositionGrayscaleReconstruction
-
- getGreen() - Method in class RGBColorBean
-
The green component value of the RGB color.
- getGreen() - Method in class RGBColor
-
The green component value of the RGB color.
- getGreen() - Method in class ThreeChannels
-
- getGroup() - Method in class RowLabels
-
an identifier for a higher-level group which the row belongs to (foreign key)
- getGroup() - Method in class AnnotationLabel
-
Specifies a group for the label (similar labels that are displayed together)
- getGroup() - Method in class ExportFeatures
-
If non-null, this file-path is used to determine the group of the file.
- getGroup() - Method in class GroupedStackBase
-
If defined, translates a file-path into a group.
- getGroup() - Method in class CSVRow
-
- getGroup() - Method in class AppendHistogram
-
- getGroupGeneratorName() - Method in class FeatureCalculationContext
-
- getGroupHeaders() - Method in class LabelHeaders
-
Headers describing the non-feature columns outputted in the CSV related to identifying the
group of a row
- getGroupMap() - Method in class GroupedSharedState
-
- getGroupNum() - Method in class RootFilePathRegEx
-
- getHeaders() - Method in class FeatureCSVMetadata
-
Headers for the CSV file
- getHeaders() - Method in class CSVReader.OpenedCSVFile
-
- getHeight() - Method in class SizeXY
-
Size in Y dimension.
- getHeight() - Method in class ImposeResolution
-
Physical pixel size of a voxel in y-dimension.
- getHistogram() - Method in class HistogramProviderUnary
-
- getHistogram() - Method in class FeatureInputHistogram
-
- getHistogram() - Method in class ConvertWithHistogram
-
If set, a histogram used in conversion to describe input intensities (across perhaps multiple
images).
- getHistogram() - Method in class SegmentChannel
-
An optional histogram of voxel intensity values which can be used by segment
- getHistogram() - Method in class PlotHistogram
-
The histogram to plot.
- getHistogram() - Method in class LevelResult
-
- getHistogram() - Method in class FromHistogram
-
If non-null, a histogram is extracted from this provider rather than the histogram from the
inputted CSV.
- getHistogramChannelIndex() - Method in class CalculateLevelBase
-
- getHistogramIndex() - Method in class IdentityImposeValueRelationToHistogram
-
- getHistogramsExtra() - Method in class ScoreVoxels
-
- getHorizontalAlign() - Method in class Overlay
-
- getId() - Method in class DictionaryProviderReference
-
- getId() - Method in class Reference
-
The identifier that uniquely determines the other feature to reference.
- getId() - Method in class FeatureProviderReference
-
The name of the feature to reference.
- getId() - Method in class FeatureResultsStatistic
-
The name of the feature, whose results will provide the statistic.
- getId() - Method in class BinarySegmentationReference
-
- getId() - Method in class FilePathProviderReference
-
- getId() - Method in class KernelDecision
-
- getId() - Method in class Reference
-
- getId() - Method in class FromChannel
-
- getId() - Method in class Reference
-
- getId() - Method in class Reference
-
- getId() - Method in class Reference
-
- getId() - Method in class ReferenceOrElse
-
- getId() - Method in class Reference
-
- getId() - Method in class FeatureIntersectingObjects
-
ID for the particular object-collection
- getId() - Method in class ExportFeatures
-
Translates an input file name to a unique ID.
- getId() - Method in class MarkBoundsReference
-
- getId() - Method in class MarkProposerReference
-
- getId() - Method in class MarkMergeProposerReference
-
- getId() - Method in class MarkSplitProposerReference
-
- getId() - Method in class Reference
-
- getId() - Method in class ReferenceOrEmpty
-
- getId() - Method in class CreateEllipse
-
- getId() - Method in class CSVRow
-
- getId() - Method in class Reference
-
- getIdentifier(T, int) - Method in interface IdentifierGetter
-
Gets the unique identifier.
- getIdentifier(T, int) - Method in class IdentifyFromIteration
-
- getIdentifier() - Method in class NamedFile
-
Unique identifier associated with the file.
- getIdentifier(Mark, int) - Method in class IdentifierFromMark
-
- getIdentifier() - Method in class Mark
-
- getIdentifier() - Method in class OverlayMark
-
- getIdentifier() - Method in class KernelWithIdentifier
-
- getIdentifier() - Method in interface Identifiable
-
- getIdentifier(Overlay, int) - Method in class IdentifierFromOverlay
-
- getIdentifier(ObjectWithProperties, int) - Method in class IdentifyDelegateToOverlays
-
- getIdentifier() - Method in class OverlayObjectMask
-
- getIdentifierSubrange() - Method in class InputArguments
-
If defined, this indicates and specifies only a subset of the naming-elements to use.
- getIdentifierSubrange() - Method in class InputContextParameters
-
If defined, this indicates and specifies only a subset of the naming-elements to use.
- getIdentifierSuffix() - Method in class QuickMultiDatasetExperiment
-
- getIdentifierSuffix() - Method in class QuickMultiDatasetStructuredExperiment
-
- getIdGenerator() - Method in class ExportObjectsFromCSV
-
- getIdGetter() - Method in class ObjectDrawAttributes
-
Gets a unique ID associated with the object
- getIfPresent(K) - Method in class LRUCache
-
Gets an value if present, but doesn't create any new entry if it's absent.
- getIgnoreContains() - Method in class AnnotationBackground
-
If non-empty, to not display any stacks in backgroundStackMap whose name contains
this string.
- getImage() - Method in class MergedPairsFeatures
-
- getImage() - Method in class PointsInitialization
-
- getImage() - Method in class InitializationWithEnergyStack
-
- getImageDimensions() - Method in class ImageFileShape
-
- getImageLabeller() - Method in class ImageAssignLabel
-
Maps a label to an image
- getImageMetadataReader() - Method in class ConvertNamedChannels
-
- getImgChannelMapCreator() - Method in class GroupFiles
-
- getIncrement() - Method in class SequenceInteger
-
Size of step to use when incrementing.
- getIndex() - Method in interface AssociatedIndex
-
The associated index.
- getIndex() - Method in class Indexable
-
- getIndex() - Method in class ChannelEntry
-
- getIndex() - Method in class KernelPointCursor
-
The index in the buffer that the kernel currently is focussed on.
- getIndex() - Method in class OutputtedFile
-
- getIndex(TreeNode) - Method in class ErrorNodeImpl
-
- getIndex() - Method in class KernelDecision
-
- getIndex() - Method in class AtIndex
-
- getIndex() - Method in class SliceAt
-
Index in z-dimension of slice to extract
- getIndex() - Method in class SpecificAxisBase
-
Specifies which principal-axis to use for calculations (0=largest eigenvalue,
1=second-largest eigenvalue etc.)
- getIndex() - Method in class IndexedRegionBase
-
- getIndex() - Method in class DistanceIndex
-
- getIndex() - Method in class OrderedRadius
-
- getIndex() - Method in class AsObject
-
- getIndex() - Method in class HOGFeature
-
Which index to return from the HOG descriptor.
- getIndexDay() - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the day, starting
from 0 for the first group.
- getIndexedRowsOrCreate(Path, ColumnDefinition) - Method in class FromCSVSharedState
-
- getIndexEnd() - Method in class ExtractSliceRange
-
Slice index to end extracting from (inclusive).
- getIndexForMemo(VoxelizedMarkMemo) - Method in class EnergyMemoList
-
- getIndexHighest() - Method in class DistanceIndexTwice
-
Highest-level index.
- getIndexHours() - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the hours, starting
from 0 for the first group.
- getIndexLowest() - Method in class DistanceIndexTwice
-
Lowest-level index.
- getIndexMinutes() - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the minutes, starting
from 0 for the first group.
- getIndexMonth() - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the month, starting
from 0 for the first group.
- getIndexNonZero() - Method in class SelectSlicesWithIndexBase
-
- getIndexSeconds() - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the seconds, starting
from 0 for the first group.
- getIndexStart() - Method in class ExtractSliceRange
-
Slice index to start extracting from (inclusive).
- getIndexYear() - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the year, starting
from 0 for the first group.
- getIndividual() - Method in class MarksWithEnergyBreakdown
-
- getInitContext() - Method in class FeedbackBeginParameters
-
- getInitialization() - Method in class InitializableBean
-
The parameters used for initialization.
- getInitialization() - Method in class ImageLabellerStringMapInitialization
-
- getInitializationType() - Method in class BeanInitializer
-
Type of parameters to be propagated, corresponding to P.
- getInitialKernel() - Method in class KernelProposer
-
- getInitialPoint() - Method in class ContiguousVoxelPath
-
- getInnerCoreDistance() - Method in class Ellipsoid
-
- getInput() - Method in class AnnotationInputManager
-
The inputs to be annotated.
- getInput() - Method in class InputOutputExperiment
-
The input-manager to specify where/which/how necessary inputs for the experiment occur.
- getInput() - Method in class InputBound
-
- getInput() - Method in class ParametersUnbound
-
- getInput() - Method in class InputManagerUnary
-
The delegate input-manager which will be circumstantially called by the current
input-manager.
- getInput() - Method in class ExperimentExecutor
-
- getInput() - Method in class MultiInputManager
-
- getInput() - Method in class AnnotationComparisonInputManager
-
- getInput() - Method in class AnnotationComparisonInput
-
- getInput() - Method in class NamedChannelsAppend
-
- getInput() - Method in class ConvertNamedChannelsToStack
-
- getInput() - Method in class FromCSVInputManager
-
- getInputContext() - Method in class InputManagerParameters
-
- getInputDebug() - Method in class BranchIfDebug
-
If defined, this provides an input to the manager when in debug-mode, rather than than
otherwise inputs.
- getInputDirectory() - Method in class FileNamerContext
-
A directory associated with the inputs, which if defined, is guaranteed to be a parent of
them all.
- getInputDirectory() - Method in class InputContextParameters
-
If defined, a directory which can be used by beans to find input
- getInputFilterExtensions() - Method in class InputContextParameters
-
A list of extensions that can be used filter inputs
- getInputFilterGlob() - Method in class InputContextParameters
-
A glob that can be used by beans to filter input
- getInputIfPresent(T) - Method in class CacheTransferSource
-
- getInputName() - Method in class MultiInputManager
-
- getInputName() - Method in class SegmentObjectsFromONNXModel
-
The name of the input in the ONNX model.
- getInputName() - Method in class QuickExperiment
-
- getInputName() - Method in class MultiInputManagerQuick
-
- getInputOutput() - Method in class InitializationContext
-
The input-output context.
- getInputOutputContext() - Method in class OptimizationContext
-
- getInputPaths() - Method in class InputContextParameters
-
A list of paths referring to specific inputs
- getInputPointShift() - Method in class ConicFitterBase
-
- getInstance() - Static method in class InterpolatorFactory
-
- getInstanceFor(Class<? extends T>) - Method in class BeanInstanceMap
-
Gets an instance from the map for a particular family-type.
- getInt(int) - Method in class VoxelBuffer
-
Gets an element from the buffer at a particular position, converting, if necessary, to an
int.
- getInt(int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
Get a value from the buffer at a particular absolute position.
- getInt(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
Get a value from the buffer at a particular relative position.
- getIntensity() - Method in class ScoreVoxels
-
- getIntensityHistogram() - Method in class BinarySegmentationParameters
-
- getIntensityProvider() - Method in class GenerateString
-
- getInterpolator() - Method in class ScaleXY
-
- getInterpolator() - Method in class OutlinePreserveRelativeSize
-
Interpolator used when scaling the background
- getInterpolator() - Method in class ScaleToSize
-
- getItem() - Method in class NamedBean
-
The item that is to be named, the underlying bean.
- getItem() - Method in class DefineSingle
-
The sole feature that forms the list.
- getItem() - Method in class PrependName
-
Provides the features and names before any prepending.
- getItem() - Method in class FeatureUnary
-
- getItem() - Method in class FeatureDeriveFromPair
-
- getItem() - Method in class ReportFeatureWrapError
-
- getItem() - Method in class ThresholdHistogram
-
- getItem() - Method in class DeriveFromPair
-
- getItem() - Method in class FeatureListProviderAggregatePair
-
For each feature in the list, a corresponding aggregate feature is created in the
output list.
- getItem() - Method in class Intensity
-
Feature to apply to the histogram
- getItem() - Method in class DerivedObject
-
- getItem() - Method in class FeatureIntersectingObjectsSingleElement
-
- getItem() - Method in class PairedWithMask
-
- getItem() - Method in class RejectIfIntensityLessThan
-
- getItem() - Method in class FeatureSingleObjectFromShared
-
- getItem() - Method in class Intensity
-
Feature to apply to the histogram
- getItem() - Method in class AsObjectMask
-
- getItem() - Method in class QuantileAcrossConnectedComponents
-
- getItem() - Method in class Rooted
-
- getItem() - Method in class CoefficientOfVarianceFromAll
-
- getItem() - Method in class MeanFromAll
-
- getItem() - Method in class Intensity
-
Feature to apply to the histogram
- getItem() - Method in class FeaturePairMemoOne
-
- getItem1() - Method in class FeatureBinary
-
Provides the first value for the binary-function.
- getItem2() - Method in class FeatureBinary
-
Provides the second value for the binary-function.
- getItemMean() - Method in class StatisticalBase
-
- getItemProportionate() - Method in class FeatureAsIndividualProportionate
-
- getItemStdDev() - Method in class StatisticalBase
-
- getIteration() - Method in class Reporting
-
- getIterations() - Method in class AnisotropicDiffusion
-
How many iterations to perform diffusion.
- getIterations() - Method in class MorphologicalOperatorBase
-
- getIterations() - Method in class ObjectCollectionProviderMorphological
-
- getIterations() - Method in class Repeat
-
The maximum number of iterations.
- getIterations() - Method in class Intersection
-
The number of dilations and erosions to apply to determine if two objects intersect
- getIterations() - Method in class IntensityMeanShellBase
-
The number of dilations and erosions to apply and whether to do in the Z dimension.
- getIterations() - Method in class Erode
-
- getIterations() - Method in class NumberRemovedVoxelsAfterClosing
-
- getIterations() - Method in class Shell
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- getIterations() - Method in class MorphologicalOperation
-
iterations for erode, dilate, open, close
- getIterations() - Method in class UniformProposal
-
- getIterations() - Method in class NumberIterationsBase
-
The number of iterations for which the number-of-marks must remain constant.
- getIterationsDilation() - Method in class MorphologicalIterations
-
Number of times to perform morphological dilation
- getIterationsErosion() - Method in class MorphologicalIterations
-
Number of times to perform morphological erosion
- getJobDescription() - Method in class SubmittedJob
-
- getJobManifest() - Method in class CoupledManifests
-
- getJobNumber() - Method in class JobDescription
-
- getJobShortName() - Method in class JobDescription
-
- getJobState() - Method in class SubmittedJob
-
- getKappa() - Method in class AnisotropicDiffusion
-
A parameter kappa associated with the diffusion functions.
- getKeep() - Method in class MergeCandidate
-
- getKeepProcessorsFree() - Method in class DebugDependentProcessor
-
How many processors to avoid using for the tasks.
- getKeepProcessorsFree() - Method in class ParallelProcessor
-
How many processors to avoid using for the tasks.
- getKernel() - Method in class KernelWithIdentifier
-
- getKernel() - Method in class WeightedKernel
-
- getKernel() - Method in class OptimizationStep
-
- getKernel() - Method in class Reporting
-
- getKernel() - Method in class KernelProposerOptionSingle
-
- getKernelAccepted() - Method in class Aggregator
-
- getKernelApplication() - Method in class DilationContext
-
How the kernel is applied to the scene.
- getKernelCalcContext() - Method in class TransformationContext
-
- getKernelFactoryList() - Method in class FeedbackBeginParameters
-
- getKernelHalfWidth() - Method in class Median
-
Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
- getKernelNegative() - Method in class KernelProposerOptionDual
-
- getKernelNoProposalDescription() - Method in class Reporting
-
- getKernelPositive() - Method in class KernelProposerOptionDual
-
- getKernelProposed() - Method in class Aggregator
-
- getKernelProposer() - Method in class SegmentWithMarkedPointProcess
-
Proposes kernel-changes during iterations of hte marked-point-processes.
- getKernelStateBridge() - Method in class TransformationAssignMode
-
- getKey() - Method in exception GetOperationFailedException
-
The key that was used in the operation that created this exception.
- getKey() - Method in class AssignFromDictionary
-
The key of the value in the dictionary that will be assigned.
- getKey() - Method in class DictionaryCondition
-
The key in the dictionary whose value is checked.
- getKey() - Method in class IfParamEqual
-
- getKey() - Method in class ParamFromCollection
-
The name of the key in the dictionary, whose corresponding value will be returned.
- getKey() - Method in class FilePathParser
-
- getKey() - Method in class RegularExpression
-
- getKey() - Method in class FromDictionary
-
- getKeyGroupID() - Method in class RegularExpression
-
- getKeyLower() - Method in class ScaleByDictionary
-
- getKeyMean() - Method in class GaussianSampler
-
The name of the key in the dictionary with the mean of the distribution.
- getKeyPrefix() - Method in class FromDictionary
-
Prefix prepended to key
- getKeyStandardDeviation() - Method in class GaussianSampler
-
The name of the key in the dictionary with the standard-deviation.
- getKeySuffix() - Method in class FromDictionary
-
- getKeyUpper() - Method in class ScaleByDictionary
-
- getLabel() - Method in class ImageLabelAnnotation
-
The label that applies to the image.
- getLabel() - Method in class StackProviderWithLabel
-
- getLabelMap() - Method in class ImageCSVLabellerInitialization
-
- getLabels() - Method in class LabelledResultsVector
-
The labels.
- getLabels() - Method in class PlotIndexBase
-
- getLabels() - Method in class ImageLabelStrategy
-
- getLabels() - Method in class LabelledResultsVectorWithThumbnail
-
The labels.
- getLastDivider() - Method in class Aggregator
-
- getLastPoints1() - Method in class MarkMergeProposer
-
- getLastPoints2() - Method in class MarkMergeProposer
-
- getLeafDirectories() - Method in class TraversalResult
-
All the directories in the bottom-most depth that was traversed.
- getLeft() - Method in class ObjectsToCompare
-
Objects on left-side of the comparison
- getLeftUnassigned() - Method in class OverlappingObjects
-
The unassigned objects in the left set.
- getLevel() - Method in class Constant
-
- getLevel() - Method in class LevelResult
-
- getLine() - Method in class CSVRow
-
- getList() - Method in class Concatenate
-
- getList() - Method in class RegExList
-
The list of
RegExes that are successively tried to be matched.
- getList() - Method in class StringMap
-
A list of mappings between a single-items in the respective sets.
- getList() - Method in class ToMultiple
-
The list of loggers to log to
- getList() - Method in class MessageLoggerList
-
- getList() - Method in class Define
-
The list that specifies features.
- getList() - Method in class DefinedNamed
-
- getList() - Method in class FeatureList
-
The list of features.
- getList() - Method in class FeatureFromList
-
The features whose results will be somehow combined, to form the result of this class.
- getList() - Method in class ArrangeRaster
-
- getList() - Method in class Combine
-
- getList() - Method in class TileWithLabels
-
- getList() - Method in class FinderExperimentFileDirectories
-
- getList() - Method in class RegionMap
-
- getList() - Method in class AddCriteriaOr
-
- getList() - Method in class FeedbackReceiverList
-
- getList() - Method in class TerminationConditionListOr
-
- getList() - Method in class Concatenate
-
- getList() - Method in class CalculateLevelListBase
-
- getList() - Method in class ObjectFilterCombine
-
A list of other filters from which the sub-classes implement filtering behaviour.
- getList() - Method in class Concatenate
-
- getList() - Method in class Sequence
-
A list of binary-segmentations that are applied successively (the output of the predecessor
becomes the input of the sucecssor)
- getList() - Method in class Concatenate
-
- getList() - Method in class SpecificAndRename
-
- getList() - Method in class FromEntries
-
- getList() - Method in class Combine
-
- getList() - Method in class Concatenate
-
- getList() - Method in class SummarizerAggregate
-
- getList() - Method in class AndList
-
- getList() - Method in class VisitSchedulerAnd
-
- getList() - Method in class VisitSchedulerUniformSample
-
- getList() - Method in class MarkProposerFromList
-
- getListAdditionalChannelProviders() - Method in class ScoreObjects
-
- getListAppend() - Method in class NamedChannelsAppend
-
- getListAppend() - Method in class MultiInputManagerQuick
-
Additional entities that are appended to the multi-input
- getListFeatures() - Method in class BinaryClassifierImageLabeller
-
- getListFromManager(MultiInputManager) - Method in class AppendDictionary
-
- getListFromManager(MultiInputManager) - Method in class AppendFilePath
-
- getListFromManager(MultiInputManager) - Method in class AppendHistogram
-
- getListFromManager(MultiInputManager) - Method in class AppendMarks
-
- getListFromManager(MultiInputManager) - Method in class AppendObjects
-
- getListFromManager(MultiInputManager) - Method in class AppendStack
-
- getListFromManager(MultiInputManager) - Method in class AppendStackDirect
-
- getListFromManager(MultiInputManager) - Method in class FilePathBaseAppendToManager
-
- getListImageFeatures() - Method in class EnergySchemeCreatorByElement
-
- getListImageFeatures() - Method in class EnergyScheme
-
- getListPaths() - Method in class SpecificPathList
-
If specified, this forms the list of paths which is provided as input.
- getListReportFeatures() - Method in class ExportReportFeatures
-
- getListStackProvider() - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- getListStackProviderMIP() - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- getLocal(int) - Method in interface BufferRetriever
-
Get a buffer at a particular index in the z-dimension.
- getLocal(int) - Method in class LocalSlices
-
- getLocalPath() - Method in class AnchorBean
-
A local path on the filesystem associated with this bean (from serialization) if defined.
- getLog() - Method in class OnlyIf
-
The logger to use if conditions are fulfilled
- getLogExperiment() - Method in class OutputExperiment
-
Where log messages that do not pertain to a specific job (input) appear.
- getLogExperimentPath() - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for the experiment in gneeral
- getLogger() - Method in class InitializableBean
-
The logger.
- getLogger() - Method in class CommonContext
-
The logger
- getLogger() - Method in class InitializationContext
-
- getLogger() - Method in class InputBound
-
- getLogger() - Method in class InputOutputContextStateful
-
- getLogger() - Method in class InputManagerParameters
-
- getLogger() - Method in class FileNamerContext
-
Logs information messages.
- getLogger() - Method in interface InputOutputContext
-
The associated logger.
- getLogger() - Method in class ReporterAggregate
-
- getLogger() - Method in class FeedbackEndParameters
-
- getLogger() - Method in class OptimizationContext
-
- getLogger() - Method in class TransformationContext
-
- getLogger() - Method in class FeatureCalculationContext
-
- getLoggerExperiment() - Method in class ExperimentFeedbackContext
-
The logger associated with the experiment.
- getLoggerExperiment() - Method in class ParametersExperiment
-
- getLoggerTaskCreator() - Method in class ParametersExperiment
-
This is a means to create new log-reporters for each task.
- getLogReporterJob() - Method in class InputBound
-
- getLogTask() - Method in class InputOutputExperiment
-
Where log messages that do pertain to a specific job (input) appear.
- getLogTaskPath() - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for a specific task
- getMainChannelIndex() - Method in class NamedChannelsQuick
-
Index of the mainChannel
- getMainChannelName() - Method in class NamedChannelsQuick
-
The name of the channel provided by the rasters in file Provider
- getMainObjectName() - Method in class MultiInput
-
- getMainObjectName() - Method in class StackWithMap
-
- getMajorAxisAngle() - Method in class EllipseStandardFormConverter
-
- getMajorAxisSlope() - Method in class EllipseStandardFormConverter
-
- getManifest() - Method in class InputBound
-
- getManifestDescription() - Method in class OutputPattern
-
A manifest-description for the directory, if defined.
- getManifestDescription() - Method in class FileType
-
- getManifestDescriptionFunction() - Method in class MarksGeneratorBase
-
- getManifestDeserializer() - Method in class CoupledManifestsInputManager
-
- getManifestExperimentInputFileSet() - Method in class CoupledManifestsInputManager
-
- getManifestFunction() - Method in class ObjectSerializerPeriodicReporter
-
- getManifestFunction() - Method in class VoxelizedMarksChangeReporter
-
- getManifestInputFileSet() - Method in class CoupledManifestsInputManager
-
- getMap() - Method in class OperationMap
-
- getMap() - Method in class OverlayProperties
-
- getMap() - Method in class ImageLabellerStringMap
-
- getMap() - Method in class ImageLabellerStringMapInitialization
-
- getMapping() - Method in class AnonymizeSharedState
-
- getMark() - Method in class FeatureInputMark
-
- getMark() - Method in class VoxelizedMarkMemo
-
The associated mark
- getMark() - Method in class OverlayMark
-
- getMark() - Method in class KernelDeath.MarkAnd
-
- getMark() - Method in class ObjectWithEllipse
-
- getMarkBounds() - Method in class MarkBoundsDefine
-
- getMarkBounds() - Method in class SegmentThresholdAboveMinBound
-
- getMarkEvaluator() - Method in class MarkProposerStrategy
-
A mark-evaluator that is added to the GUI to support this annotation
- getMarkFactory() - Method in class MarkEvaluator
-
- getMarkFactory() - Method in class KernelCalculationContext
-
- getMarkFactory() - Method in class MarkFactoryContext
-
- getMarkFactory() - Method in class OptimizationContext
-
- getMarkFactory() - Method in class SegmentWithMarkedPointProcess
-
Creates a new mark, before perhaps further manipulations by a kernel.
- getMarkFactory() - Method in class FitPointsFromObjects
-
- getMarkFromMarksProposer() - Method in class KernelSplit
-
- getMarkProposer() - Method in class MarkProposerStrategy
-
- getMarkProposer() - Method in class FromMarkProposer
-
- getMarkProposer() - Method in class MergeMarkEllipse
-
- getMarkProposer() - Method in class KernelBirthAndKill
-
- getMarkProposer() - Method in class KernelExchange
-
- getMarkProposer() - Method in class KernelBirthVoxelized
-
- getMarkProposerAdditionalBirth() - Method in class KernelBirthAndKill
-
- getMarkProvider() - Method in class CreateMarkFromPoints
-
- getMarkProvider() - Method in class ReportFeatureOnMark
-
- getMarkProvider() - Method in class FromSingleMark
-
- getMarkProvider() - Method in class RequireFeatureRelationThreshold
-
- getMarkRmv() - Method in class KernelDeath
-
- getMarks() - Method in class RandomCollectionWithAddCriteria
-
- getMarks() - Method in class FeatureInputMarkCollection
-
- getMarks() - Method in class IndexableMarksWithEnergy
-
- getMarks() - Method in class MarksWithEnergyBreakdown
-
- getMarks() - Method in class MarksWithTotalEnergy
-
The marks
- getMarks() - Method in class VoxelizedMarksWithEnergy
-
- getMarks() - Method in class ReportFeatureOnMarks
-
- getMarks() - Method in class MarksWithDisplayStack
-
- getMarks() - Method in class ColoredMarks
-
- getMarks() - Method in class MarkCollection
-
The underlying
List that stores the
Marks in the collection.
- getMarks() - Method in class FromMarks
-
- getMarks() - Method in class ScaleXY
-
- getMarks() - Method in class RetrieveSingleMarkOnly
-
- getMarks() - Method in class ColoredMarks
-
- getMarks() - Method in class MarksFromPartition
-
- getMarksAfter() - Method in class Reporting
-
- getMarksAfterOptional() - Method in class Reporting
-
- getMarksColored() - Method in class ColoredMarksWithDisplayStack
-
- getMarksProposer() - Method in class KernelInitialMarksFromPartition
-
- getMarksProposer() - Method in class KernelInitialMarksProposed
-
- getMarksProposer() - Method in class KernelInitialMarksVoxelized
-
- getMarksReject() - Method in class DualMarksAnnotation
-
Marks covering area that should be rejected, can be null
- getMarksWithTotalEnergy() - Method in class MarksWithEnergyBreakdown
-
- getMask() - Method in class MaskProviderUnary
-
- getMask() - Method in class FromMaskBase
-
- getMask() - Method in class UnaryWithMaskBase
-
- getMask() - Method in class ScoreVoxels
-
- getMask() - Method in class FromChannel
-
- getMask() - Method in class SegmentChannel
-
An optional mask which restricts the algorithm to only parts of the channel where the mask
has an on voxel
- getMask() - Method in class ConnectedComponentsFromMask
-
- getMask() - Method in class AndObjectsWithMasks
-
- getMask() - Method in class FromMask
-
- getMask() - Method in class SegmentChannel
-
- getMask() - Method in class ColoredMask
-
- getMask() - Method in class FromChannelOrMask
-
A mask that is provided to the stack.
- getMask() - Method in class PairedWithMask
-
- getMask() - Method in class MaskAsSingleObject
-
- getMask() - Method in class FillHoles
-
- getMask() - Method in class CheckMarkWithMask
-
- getMask() - Method in class FindPointOnContourWalk
-
- getMask() - Method in class XYOrientationExtendToZ
-
- getMaskContour() - Method in class TraverseOuterContourOnImage
-
- getMaskElse() - Method in class IfPredicateBase
-
Returned instead of mask if the predicate is not satisfied
- getMaskFilled() - Method in class TraverseOuterContourOnImage
-
- getMaskFilled() - Method in class XYOrientationExtendToZ
-
- getMaskIndex() - Method in class SurfaceSizeMaskNonZero
-
- getMaskValue() - Method in class ExportImageHistograms
-
What voxel value to read as "On" in the mask above.
- getMaskValue() - Method in class OverlapMaskBase
-
- getMatch() - Method in class FilterCSVColumn
-
- getMatch() - Method in class MatchedAppendCsv
-
- getMatcher() - Method in class SearchDirectory
-
- getMatcher() - Method in class MatchExtensions
-
- getMatcher() - Method in class RelationWithMatches
-
- getMatcher() - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- getMatcher() - Method in class Match
-
- getMatches() - Method in class MatchedObject
-
The matches associated with the source-object
- getMatrix() - Method in class CostMatrix
-
A two-dimensional array mapping the costs from first to second.
- getMatrix() - Method in class RotationMatrix
-
The underlying matrix used internally in the rotation-matrix.
- getMax() - Method in interface Progress
-
Retrieves the maximum value of progress that is possible.
- getMax() - Method in class ProgressConsole
-
- getMax() - Method in class ProgressIgnore
-
- getMax() - Method in class ProgressIncrement
-
Retrieves the maximum value of progress that is possible.
- getMax() - Method in class BoundMinMax
-
- getMax() - Method in class ResolvedBound
-
- getMax() - Method in class PointListBase
-
- getMax() - Method in class ScaleByMinMaxValue
-
- getMax() - Method in class ClampHistogramMax
-
- getMax() - Method in class UnitsWithinRange
-
Maximum-boundary for acceptable range
- getMax() - Method in class OutsideRange
-
- getMax() - Method in class MaxOverlapRatio
-
- getMax() - Method in class InvertedMax
-
- getMax() - Method in class CompareWithRangeFeature
-
Calculates maximally-allowed range boundary
- getMax() - Method in class RangeCompareFromScalars
-
Boundary value indicating maximally-allowed range value
- getMaxCost() - Method in class MultipleComparer
-
The maximum cost (as calculated by featureEvaluator) to accept when creating an
assignment between objects.
- getMaxCost() - Method in class FeatureCostAssigner
-
- getMaxDirectoryDepth() - Method in class SearchDirectory
-
If non-negative the max depth of directories.
- getMaxDirectoryDepth() - Method in class PathMatchConstraints
-
Limits on the depth of how many sub-directories are recursed
- getMaxDirectoryDepth() - Method in class ExperimentResultsExperimentStructure
-
- getMaxDistance() - Method in class MergeWithOptionalDistanceConstraint
-
An optional maximum distance
- getMaxDistance() - Method in class CostOverlapWithinMidpointDistance
-
- getMaxDistance() - Method in class FindPointOnContourWalk
-
- getMaxDistanceBetweenMinima() - Method in class AddDistanceTransform
-
- getMaxDistanceCOG() - Method in class MergeSpatialClusters
-
The maximum distance allowed between center-of-gravities of objects
- getMaxDistanceDeltaContour() - Method in class AddDistanceTransform
-
The maximum distance allowed between two seeds in terms of their values in the distance map
- getMaxDistanceDeltaContour() - Method in class MergeSpatialClusters
-
The maximum distance allowed between the 'distance from contour' values provided from the
distanceMap for each point.
- getMaxDistanceProposer() - Method in class VisitSchedulerMaxDistanceAlongContour
-
- getMaxDistanceZ() - Method in class XYOrientationExtendToZ
-
- getMaximumIndex() - Method in interface IndexRange
-
The maximum index in the range.
- getMaximumNumberChannels() - Method in class IntensityMoments
-
An upper limit on the number of channels in the energy-stack for which we create features.
- getMaxInstant() - Method in class ClusterIdentifier
-
Maximum timestamp in cluster.
- getMaxIter() - Method in class Repeat
-
- getMaxIter() - Method in class Repeat
-
- getMaxIter() - Method in class Repeat
-
- getMaxIter() - Method in class RadiiProposerRepeat
-
- getMaxNumberItems() - Method in class Limit
-
- getMaxNumberItems() - Method in class Limit
-
- getMaxNumberProcessors() - Method in class TaskArguments
-
Suggests a maximum number of processors (CPUs) for a task.
- getMaxNumberProcessors() - Method in class DebugDependentProcessor
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- getMaxNumberProcessors() - Method in class ParallelProcessor
-
Theoretical maximum number of (CPU) processors to use in parallel.
- getMaxNumberProcessors() - Method in class QuickMultiDatasetExperiment
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- getMaxNumberProcessors() - Method in class QuickMultiDatasetStructuredExperiment
-
- getMaxNumItems() - Method in class LimitWithDirectory
-
- getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundDegrees
-
- getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundPhysicalExtent
-
- getMaxResolved(Optional<Resolution>, boolean) - Method in class BoundUnitless
-
- getMaxResolved(Optional<Resolution>, boolean) - Method in class MarkBounds
-
- getMaxSize() - Method in class Mser
-
- getMaxSplitGroups() - Method in class CompareAnnotations
-
- getMaxTime() - Method in class ClusterIdentifier
-
Gets the latest date-time in the cluster.
- getMaxValue() - Method in class Histogram
-
Maximum possible value in the histogram (inclusive).
- getMaxValue() - Method in class ConsistentChannelChecker
-
- getMaxVar() - Method in class Mser
-
- getMaxVolume() - Method in class FillHoles
-
- getMaxX() - Method in class Box
-
Maximum X coordinate inclusive.
- getMaxY() - Method in class Box
-
Maximum Y coordinate inclusive.
- getMaxZ() - Method in class Box
-
Maximum Z coordinate inclusive.
- getMean() - Method in class MeanScale
-
The mean.
- getMean(int) - Method in class ImageMoments
-
Get the mean-value for a particular axis.
- getMedianRadiusMeters() - Method in class AddEdgeFilters
-
- getMemoForIndex(int) - Method in class VoxelizedMarksWithEnergy
-
- getMemoForIndex(int) - Method in class EnergyMemoList
-
- getMemoForIndex(int) - Method in class MemoList
-
- getMemoForIndex(int) - Method in interface MemoForIndex
-
- getMemoForMark(Mark) - Method in class VoxelizedMarksWithEnergy
-
- getMemoForMark(MarkCollection, Mark) - Method in class EnergyMemoList
-
- getMemoized() - Method in class FinderSerializedObject
-
Provides a memoized (cached) means of access the results of the finder
- getMerge() - Method in class MergeCandidate
-
- getMerged() - Method in class FeatureInputPairObjects
-
Returns a merged version of the two-objects available (or null if not available)
- getMergedOptional() - Method in class FeatureInputPairObjects
-
- getMergedPosTolerance() - Method in class MergeMarkEllipse
-
- getMergeMarkProposer() - Method in class KernelMerge
-
- getMessage() - Method in exception GetOperationFailedException
-
A message describing the failure.
- getMessage() - Method in class ReportFeatureWrapError
-
- getMessageLogger() - Method in class InputOutputContextStateful
-
- getMessageNoInputs() - Method in class InputOutputExperiment
-
A message written to the logger if no inputs exist for the experiment, and it thus ends
early.
- getMessageReporter() - Method in interface InputOutputContext
-
The associated message reporter.
- getMessages() - Method in class ConvertedInput
-
Any messages written to the log during conversion.
- getMetadata() - Method in class FeatureInputImageMetadata
-
The image metadata.
- getMethod() - Method in class AutoLocalThreshold
-
- getMethod() - Method in class ThresholderAutoIJ
-
One of the following strings to identify ImageJ's thresholding algorithms (or an empty string
for the default).
- getMethod() - Method in class CopyFiles
-
How the copying occurs from source to destination file.
- getMin() - Method in interface Progress
-
Retrieves the minimum value of progress that is possible.
- getMin() - Method in class ProgressConsole
-
- getMin() - Method in class ProgressIgnore
-
- getMin() - Method in class ProgressIncrement
-
Retrieves the minimum value of progress that is possible.
- getMin() - Method in class BoundMinMax
-
- getMin() - Method in class ResolvedBound
-
- getMin() - Method in class PointListBase
-
- getMin() - Method in class ScaleByMinMaxValue
-
- getMin() - Method in class UnitsWithinRange
-
Minimum-boundary for acceptable range
- getMin() - Method in class OutsideRange
-
- getMin(Function<FileDetails, Optional<Integer>>) - Method in class ParsedFilePathBag
-
- getMin() - Method in class RadiiMinRatio
-
- getMin() - Method in class CompareWithRangeFeature
-
Calculates minimally-allowed range boundary
- getMin() - Method in class RangeCompareFromScalars
-
Boundary value indicating minimally-allowed range value
- getMinConfidence() - Method in class ThresholdConfidence
-
The minimum confidence of an element for its object-mask to be initially included for
consideration (before merging).
- getMinConfidence() - Method in class DecodeMaskRCNN
-
Only proposals outputted from the model with a score greater or equal to this threshold are
considered.
- getMinConfidence() - Method in class DecodeEAST
-
Proposed bounding boxes below this confidence interval are removed from consideration.
- getMinDiff() - Method in class MeanIntensityDifference
-
- getMinDifference() - Method in class Difference
-
A minimum difference, below which 0.0 is returned
- getMinDifference() - Method in class DifferenceCalculateLevelStandardDeviation
-
- getMinDiversity() - Method in class Mser
-
- getMinimaImposition() - Method in class ImposeMinima
-
- getMinimumBoundingBoxVolume() - Method in class FloodFillEachIntensityLevel
-
Only objects whose bounding-box volume is greater or equal to this threshold are included.
- getMinimumIndex() - Method in interface IndexRange
-
The minimum index in the range.
- getMinimumPerCluster() - Method in class ClusterByTimestamp
-
The minimum number of files that must exist for a cluster.
- getMinInstant() - Method in class ClusterIdentifier
-
Minimum timestamp in cluster.
- getMinIntensity() - Method in class RejectIfIntensityLessThan
-
- getMinIntensity() - Method in class ThresholderSimpleFillHoles2D
-
Intensity for thresholding
- getMinIntensityValue() - Method in class MorphologicalOperatorBase
-
- getMinMaskValue() - Method in class DecodeMaskRCNN
-
Only voxels with a value greater or equal to this threshold are considered as part of the
mask.
- getMinMaxIgnoreBeforeIndex() - Method in class LinePlot
-
- getMinNumberObjects() - Method in class DiscardOutliers
-
- getMinNumberPoints() - Method in class SplitContourAtSaddlePoints
-
If a contour has less than this number of points, we don't split it, and return it as-is
- getMinNumberVoxels() - Method in class SplitIntoSquares
-
Only includes squares that have at least this number of voxels.
- getMinNumberVoxels() - Method in class ConnectedComponentsFromBinarySegmentation
-
- getMinNumberVoxels() - Method in class ThresholdConfidence
-
The minimum number of voxels that must exist in a connected-component to be included.
- getMinNumPoints() - Method in class CreateMarkFromPoints
-
- getMinNumPoints() - Method in class PointsFitterToMark
-
If an object has fewer points than before being fitted, we ignore
- getMinNumSlices() - Method in class XYOrientationExtendToZ
-
- getMinNumZSlices() - Method in class AtLeastZSlices
-
- getMinorAxisAngle() - Method in class EllipseStandardFormConverter
-
- getMinorAxisSlope() - Method in class EllipseStandardFormConverter
-
- getMinOverlap() - Method in class CostOverlapWithinMidpointDistance
-
- getMinRadius() - Method in class LinearLeastSquaresEllipseFitter
-
- getMinRadius() - Method in class LinearLeastSquaresEllipsoidFitter
-
- getMinRatio() - Method in class DiscardOutliers
-
- getMinResolution() - Method in class MinimumXYResolution
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class BoundDegrees
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class BoundPhysicalExtent
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class BoundUnitless
-
- getMinResolved(Optional<Resolution>, boolean) - Method in class MarkBounds
-
- getMinSize() - Method in class Mser
-
- getMinTime() - Method in class ClusterIdentifier
-
Gets the earliest date-time in the cluster.
- getMinusOne() - Method in class SlidingBuffer
-
The voxel-buffer for the slice with the currently selected slice's index -1 or null
if it's the first slice.
- getMinVal() - Method in class FeatureValueCheckMark
-
- getMinVolume() - Method in class ConnectedComponentsFromMask
-
- getMinVolume() - Method in class VolumeMin
-
- getMinVolumeConnectedComponent() - Method in class AddDistanceTransform
-
- getMinX() - Method in class Box
-
Minimum X coordinate inclusive.
- getMinY() - Method in class Box
-
Minimum Y coordinate inclusive.
- getMinZ() - Method in class Box
-
Minimum Z coordinate inclusive.
- getModelBinaryPath() - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb extension, relative
to the models/ directory in the Anchor distribution.
- getModelDirectory() - Method in class CommonContext
-
Directory where machine-learning models can be found
- getModelDirectory() - Method in class InputArguments
-
- getModelDirectory() - Method in class InputOutputContextStateful
-
- getModelDirectory() - Method in class ImageInitialization
-
- getModelDirectory() - Method in interface InputOutputContext
-
An input-directory in which models are stored.
- getModelDirectory() - Method in class FeatureCalculationContext
-
- getModelPath() - Method in class SegmentObjectsFromONNXModel
-
Relative-path to the model file in ONNX form, relative to the models/ directory in the
Anchor distribution.
- getModelPool() - Method in class SharedStateSegmentInstance
-
- getModelTextGraphPath() - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb.txt extension,
relative to the models/ directory in the Anchor distribution.
- getModificationTime() - Method in class ImageFileAttributes
-
The last modified timestamp on the file the image was loaded from.
- getMultipleComparer() - Method in class MarkProposerStrategy
-
- getMultipleOf() - Method in class FitTo
-
The eventual width and height of the image must be a multiple of this number.
- getMultiplyBy() - Method in class DistanceTransform3D
-
- getName() - Method in class FromXMLList
-
The name of the file in the current working directory WITHOUT THE .xml EXTENSION
- getName() - Method in class NamedBean
-
The name associated with item.
- getName() - Method in class RootPath
-
The name of the root-path, which need not be unique in itself.
- getName() - Method in interface NameValue
-
The associated name.
- getName() - Method in class SimpleNameValue
-
- getName() - Method in class ExperimentIdentifierConstant
-
- getName() - Method in class ChannelEntry
-
- getName() - Method in class OptionalNameValue
-
An optional-name.
- getName() - Method in class IncreasingIntegers
-
- getName() - Method in class IncrementingIntegers
-
- getName() - Method in class SequenceType
-
- getName() - Method in class StringsWithoutOrder
-
- getName() - Method in class NamedPath
-
A unique name associated with the path
- getName() - Method in class Circle
-
- getName() - Method in class Ellipse
-
- getName() - Method in class Ellipsoid
-
- getName() - Method in class Sphere
-
- getName() - Method in class Mark
-
- getName() - Method in class LineSegment
-
- getName() - Method in class PointList
-
- getName() - Method in class Polygon
-
- getName() - Method in class PolygonCurve
-
- getName() - Method in class RotatableBoundingBox
-
- getName() - Method in class Kernel
-
- getName() - Method in class WeightedKernel
-
- getName() - Method in class NamedChannel
-
- getName() - Method in class AdjacentFile
-
A name to describe the adjacent file
- getName() - Method in class FilePathAppendBase
-
The name of the appended entity
- getNameLeft() - Method in class AnnotationComparisonInputManager
-
- getNamer() - Method in class GroupFiles
-
- getNamer() - Method in class RemoveExtension
-
- getNamer() - Method in class SubsetRangeIfRequested
-
The namer that is called to provide names that are subsetted.
- getNamer() - Method in class NamedFilesBase
-
- getNamer() - Method in class QuickBase
-
Assigns each input a unique compact name.
- getNameRight() - Method in class AnnotationComparisonInputManager
-
- getNames() - Method in class StatisticsToExport
-
- getNames() - Method in class NamedFeatureCalculatorMulti
-
- getNames() - Method in class AnnotationComparisonInput
-
- getNameSubrange() - Method in class FileNamerContext
-
If defined, this indicates and specifies only a subset of the naming-elements to use.
- getNaming() - Method in class CopyFiles
-
How an output name (and path) is selected for an input file.
- getNamingSharedState() - Method in class RecordingCounter
-
- getNavigateHigherDirectories() - Method in class MultiFileReader
-
Search x number directories higher than file.
- getNoProposalReason() - Method in class KernelDecision
-
- getNumberBins() - Method in class HOGParameters
-
The number of bins in each histogram for a cell.
- getNumberChannels() - Method in class EnergyStack
-
The number of channels in the stack.
- getNumberChannels() - Method in class EnergyStackWithoutParameters
-
The number of channels in the stack.
- getNumberChannels() - Method in class DisplayStack
-
The number of channels in the stack.
- getNumberChannels() - Method in class ImageMetadata
-
The number of channels in the image.
- getNumberChannels() - Method in class Stack
-
The number of channels in the stack.
- getNumberChannels() - Method in class StackNotUniformSized
-
The number of channels in the
Stack.
- getNumberChannels() - Method in class ScaleableBackground
-
Number of channels in the stack
- getNumberChannels() - Method in class ForceNumberChannels
-
- getNumberChannels() - Method in class ImageFileShape
-
- getNumberChannelsPerArray() - Method in class ImageFileEncoding
-
The total number of channels found in any one buffer.
- getNumberColors() - Method in class TiffTimeSeries
-
- getNumberColumns() - Method in class Tile
-
The number of columns to use in the table produced when tiling.
- getNumberConverter() - Method in class AnonymizeSharedState
-
- getNumberDecimalPlaces() - Method in class FeatureCostAssigner
-
- getNumberDigits() - Method in class IncrementingNumber
-
Number of digits in the number, with leading zeros as necessary.
- getNumberDilations() - Method in class LevelPerObjectIndependently
-
- getNumberDimensions() - Method in class RotationMatrix
-
The number of dimensions in the rotation-matrix.
- getNumberElements() - Method in class IncreasingIntegers
-
- getNumberElements() - Method in class IncrementingIntegers
-
- getNumberElements() - Method in class SequenceType
-
- getNumberElements() - Method in class StringsWithoutOrder
-
- getNumberFrames() - Method in class ImageMetadata
-
The number of frames (separate images representing different points in a time-series) in the
image.
- getNumberFrames() - Method in class ForceNumberFrames
-
- getNumberFrames() - Method in class ImageFileShape
-
- getNumberGPUProcessors() - Method in class ParallelProcessor
-
How many GPU processors to use when this is possible as a substitute for a CPU processor
- getNumberKernels() - Method in class KernelProposer
-
- getNumberLevelsGrouping() - Method in class CompareAnnotations
-
- getNumberLoopPoints() - Method in class SplitContourAtSaddlePoints
-
- getNumberParentOperations() - Method in class RecordedExecutionTimes.RecordedOperation
-
The number of parent operations.
- getNumberParentOperations() - Method in class RunningSumParented
-
The number of parent operations.
- getNumberPoints() - Method in class LinePlot
-
- getNumberRows() - Method in class Tile
-
The number of rows to use in the table produced when tiling.
- getNumberSeries() - Method in class PlotIndexBase
-
- getNumberSlices() - Method in class ImageFileShape
-
- getNumberSubdirectories() - Method in class LastDirectories
-
How many directories to include in the name.
- getNumCols() - Method in class TileWithLabels
-
- getNumColsUsed() - Method in class TableItemArrangement
-
- getNumMarks() - Method in class FromMarkProposer
-
- getNumRowsUsed() - Method in class TableItemArrangement
-
- getObject() - Method in class Found
-
The found object.
- getObject() - Method in class FeatureInputSingleObject
-
- getObject() - Method in class OverlayObjectMask
-
- getObject() - Method in class LevelResult
-
- getObject() - Method in class ObjectVertex
-
- getObject() - Method in class ObjectWithEllipse
-
- getObject1() - Method in class FeatureInputPairMemo
-
- getObject2() - Method in class FeatureInputPairMemo
-
- getObjectMatcher() - Method in class Bridge
-
Used to match each intermediary-object to a final-object
- getObjects() - Method in class ObjectCollectionProviderUnary
-
- getObjects() - Method in class FeatureInputObjectCollection
-
- getObjects() - Method in class OutputFeatureTable
-
The objects for which features are calculated.
- getObjects() - Method in class ReportFeatureOnObjectsBase
-
- getObjects() - Method in class DistanceTransformForEachObject3D
-
- getObjects() - Method in class LevelPerObjectBase
-
The objects for whom a level is calculated
- getObjects() - Method in class UnaryWithObjectsBase
-
- getObjects() - Method in class GenerateToMatchObjects
-
- getObjects() - Method in class FromObjects
-
- getObjects() - Method in class IntersectsWith
-
- getObjects() - Method in class Always
-
- getObjects() - Method in class Intersection
-
- getObjects() - Method in class Permute
-
- getObjects() - Method in class ColoredObjects
-
Objects to draw on a background
- getObjects() - Method in class ObjectAggregationBase
-
- getObjects() - Method in class ColoredObjectCollection
-
The objects in the collection.
- getObjects() - Method in class FromObjects
-
- getObjects() - Method in class ObjectAsPoints
-
- getObjects() - Method in class IncludeRandomObjects
-
- getObjects() - Method in class PointsFromObjects
-
- getObjects() - Method in class FromObjects
-
- getObjects() - Method in class ExportObjectsBase
-
- getObjects() - Method in class PointsFitterToMark
-
- getObjects1() - Method in class MergeTwoCollectionsItemwise
-
First collection with items to be merged
- getObjects2() - Method in class MergeTwoCollectionsItemwise
-
Second collection with items to be merged
- getObjectsBlue() - Method in class ThreeColoredObjects
-
- getObjectsContainer() - Method in class WithContainerBase
-
- getObjectsElse() - Method in class ReferenceOrElse
-
- getObjectsGreater() - Method in class GreaterIntersectionWith
-
- getObjectsGreen() - Method in class ThreeColoredObjects
-
- getObjectsGrouped() - Method in class FilterByGroup
-
- getObjectsLesser() - Method in class GreaterIntersectionWith
-
- getObjectsRed() - Method in class ThreeColoredObjects
-
- getObjectsRejected() - Method in class ObjectCollectionProviderFilterBase
-
- getObjectsSeeds() - Method in class SegmentChannel
-
- getObjectsSeeds() - Method in class SegmentWithSeeds
-
- getObjectsSource() - Method in class AssignFromIntersectingObjects
-
- getObjectsSource() - Method in class SegmentWithSeeds
-
- getObjectsSplitBy() - Method in class SplitByObjects
-
- getObjectsTarget() - Method in class AssignFromIntersectingObjects
-
- getOff() - Method in class BinaryValuesByte
-
The byte representation of the value for off.
- getOff() - Method in class BinaryValuesInt
-
The integer representation of the value for off.
- getOffset() - Method in class ClusterIdentifier
-
The offset to assume the time-stamp belongs in.
- getOn() - Method in class BinaryValuesByte
-
The byte representation of the value for on.
- getOn() - Method in class BinaryValuesInt
-
The integer representation of the value for on.
- GetOperationFailedException - Exception in org.anchoranalysis.core.index
-
When a get operation fails for a particular key.
- GetOperationFailedException(Exception) - Constructor for exception GetOperationFailedException
-
Creates with only a cause, omitting a key and a message.
- GetOperationFailedException(int, String) - Constructor for exception GetOperationFailedException
-
Creates with a message, but no cause - with an integer key.
- GetOperationFailedException(String, String) - Constructor for exception GetOperationFailedException
-
Creates with a message, but no cause - with
a String key.
- GetOperationFailedException(int, Throwable) - Constructor for exception GetOperationFailedException
-
Creates with a cause, but no message - with an integer key.
- GetOperationFailedException(String, Throwable) - Constructor for exception GetOperationFailedException
-
Creates with a cause, but no message - with
a String key.
- getOperationIdentifier() - Method in class RecordedExecutionTimes.RecordedOperation
-
An (unique) identifier for the operation.
- getOptimization() - Method in class SegmentWithMarkedPointProcess
-
The optimization-scheme that determines which configurations are accepted/rejected from one
iteration to the next.
- getOptional(String) - Method in interface NamedProvider
-
Retrieves the item if it exists, or returns
Optional.empty() if it doesn't exist.
- getOptional(String) - Method in class NamedProviderBridge
-
- getOptional(String) - Method in class NamedProviderCombine
-
- getOptional(String) - Method in class NameValueMap
-
- getOptional(String) - Method in class EagerEvaluationStore
-
- getOptional(String) - Method in class LazyEvaluationStore
-
- getOptional(String) - Method in class SharedFeatures
-
- getOptional(String) - Method in class NamedStacks
-
- getOptional(String) - Method in class WrapStackAsTimeSequenceStore
-
- getOptionList() - Method in class KernelProposer
-
- getOptions() - Method in class BioformatsReader
-
Options that influence how stack is read.
- getOptions() - Method in class ReadOptionsDelegate
-
- getOrCalculate(T) - Method in class ResolvedPart
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a
cached-result from previously.
- getOrCalculate(T, U) - Method in class ResolvedPartMap
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a
cached-result from a previous execution.
- getOrCalculate(T) - Method in class CalculationPart
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a
cached-result from previously.
- getOrCalculate(T, U) - Method in class CalculationPartMap
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a
cached-result from a previous execution.
- getOrCreate(Class<?>) - Method in class SharedObjects
-
Gets an existing store, or creates a new one
- getOrientation() - Method in class Ellipse
-
- getOrientation() - Method in class Ellipsoid
-
- getOrientationProposer() - Method in class OrientationAndRadiiProposer
-
- getOrientationXYProposer() - Method in class XYOrientationExtendToZ
-
- getOriginal() - Method in class OverlappingObject
-
Original unscaled element before any operations
- getOrLog(String, Logger) - Method in interface Findable
-
Gets an object or otherwise logs a message describing what went wrong.
- getOrLog(String, Logger) - Method in class Found
-
- getOrLog(String, Logger) - Method in class NotFound
-
- getOrNull(U) - Method in class CalculationPartMap
-
Gets an existing result for the current input from the cache.
- getOtherwise() - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is not selected.
- getOutlineColor() - Method in class SegmentInstanceWithModel
-
The color of the outline.
- getOutlinePixelsRetriever() - Method in class TraversePointsOnContour
-
- getOutlinePixelsRetrieverReverse() - Method in class TraversePointsOnContour
-
- getOutlineWidth() - Method in class BoundingBoxOutline
-
- getOutlineWidth() - Method in class Outline
-
- getOutlineWidth() - Method in class CompareAnnotations
-
How many pixels should the outline be around objects.
- getOutlineWidth() - Method in class AtScale
-
- getOutlineWidth() - Method in class ColoredBase
-
The width of the outline (only relevant if outline==true.
- getOutlineWidth() - Method in class OutlinePreserveRelativeSize
-
The width of the outline.
- getOutlineWidth() - Method in class SegmentInstanceWithModel
-
The width of the outline.
- getOutlineWidth() - Method in class VisualizeOnBackground
-
- getOutlineWidth() - Method in class ExportObjectsAsCroppedImages
-
- getOutPath() - Method in class InsertRegExGroups
-
Constructs a path as an output, replacing $1, $2 etc.
- getOutput() - Method in class OutputExperiment
-
The output-manager that specifies how/where/which elements occur duing outputting.
- getOutput() - Method in class ExperimentExecutor
-
- getOutput() - Method in class QuickMultiDatasetExperiment
-
- getOutputDirectory() - Method in class Outputter
-
- getOutputDirectory() - Method in class OutputterChecked
-
- getOutputDirectory() - Method in class OutputPrefixerSettings
-
A directory indicating where inputs can be located
- getOutputEnabledDelta() - Method in class OutputArguments
-
Additions/subtractions of outputs for the experiment supplied by the user.
- getOutputName() - Method in class ToTextFileBase
-
The name to use (without extension) for the text-file log
- getOutputName() - Method in class FeatureCSVMetadata
-
The output name for the features CSV.
- getOutputName() - Method in class OutputtedFile
-
- getOutputName() - Method in class OutputNameStyle
-
An identifier used in rules to determine if an output is enabled or not.
- getOutputName() - Method in class PeriodicSubdirectoryReporter
-
- getOutputName() - Method in class MinimalExecutionTimeStatsReporter
-
- getOutputName() - Method in class VoxelizedMarksChangeReporter
-
- getOutputNameStyle() - Method in class OutputPattern
-
- getOutputNameStyle() - Method in class FromOutputName
-
- getOutputPattern() - Method in class BoundOutputter
-
- getOutputRGBOutline() - Method in class ExportObjectsAsCroppedImages
-
- getOutputRGBOutlineFlattened() - Method in class ExportObjectsAsCroppedImages
-
- getOutputsDisabled() - Method in class SpecificDisabled
-
The names of the outputs that are disbled.
- getOutputsEnabled() - Method in class SpecificEnabled
-
The names of the outputs that are enabled.
- getOutputsEnabled() - Method in class OutputManager
-
Which outputs are enabled or not enabled.
- getOutputsEnabled() - Method in class OutputterChecked
-
Which outputs are enabled or not enabled.
- getOutputsEnabled() - Method in class ElementOutputter
-
Which outputs are enabled or not enabled.
- getOutputStackProvider() - Method in class ImageAssignLabel
-
If it's set, a stack is generated that is outputted into subdirectory corresponding to the
groupIdentifier.
- getOutputter() - Method in class InitializationContext
-
- getOutputter() - Method in class InputBound
-
- getOutputter() - Method in class InputOutputContextStateful
-
- getOutputter() - Method in class ParametersExperiment
-
- getOutputter() - Method in class BoundOutputter
-
The outputter to be used for the sequence.
- getOutputter() - Method in interface InputOutputContext
-
An outputter that writes to the particular output-directory.
- getOutputter() - Method in class ElementOutputter
-
The outputter for writing the element.
- getOutputter() - Method in class OptimizationContext
-
- getOutputterFor(String) - Method in class SharedStateFilteredImageOutput
-
groupIdentifierFor should always called at least once before getOutputManagerFor
- getOutputWriteSettings() - Method in class OutputManager
-
General settings (default file extensions, colors etc.) for outtping files.
- getOutputWriteSettings() - Method in class QuickExperiment
-
- getOutside() - Method in class UnitsWithinRange
-
Returned as a constant if a value lies otside the range
- getOutsideKernelPolicy() - Method in class KernelApplicationParameters
-
How to handle voxels that appear in a neighborhood that lies outside the scene boundaries.
- getOverlapRatioThreshold() - Method in class KernelBirthAndKill
-
- getOverlays() - Method in class ColoredOverlayCollection
-
- getOverlays() - Method in class IndexableOverlays
-
- getPadding() - Method in class TextStyle
-
Padding added around the text in both dimensions if a default size is inferred (ignored if an
explicit size is specified )
- getPadding() - Method in class DrawCroppedObjectsGenerator
-
- getPadding() - Method in class ExportObjectsBase
-
Padding placed on each side of the outputted image (if it's within the image)
- getPaddingXY() - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in XY
directions
- getPaddingZ() - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in Z direction
- getPair() - Method in class MergedPairsFeatures
-
- getPair() - Method in class EnergyPair
-
- getPair() - Method in class MarksWithEnergyBreakdown
-
Every combination of interactions between marks and the associated energy
- getPairAddCriteria() - Method in class EnergySchemeCreatorByElement
-
- getPairAddCriteria() - Method in class EnergyScheme
-
- getPairCollection() - Method in class KernelMerge
-
- getPairsFor(Mark) - Method in class RandomCollectionWithAddCriteria
-
- getPairTypeClass() - Method in class RandomCollectionWithAddCriteria
-
- getParameters() - Method in class EnergyStack
-
The associated parameters.
- getParameters() - Method in class HOGDescriptor
-
Parameters used for calculating HOG
- getParameters() - Method in class HOGFeature
-
Parameters used for calculating HOG.
- getParametersExperiment() - Method in class ParametersUnbound
-
- getParamPrefix() - Method in class PermuteFeatureSequenceInteger
-
- getParent() - Method in class ErrorNodeImpl
-
- getParentDirectory() - Method in class MutableDirectory
-
- getParentDirectory() - Method in class OutputtedFile
-
- getParentDirectoryCreator() - Method in class OutputterTarget
-
- getParentOutputter() - Method in class PeriodicSubdirectoryReporter
-
- getPartition() - Method in class MarksFromPartition
-
- getPath() - Method in class AnnotationWithStrategy
-
Path to annotation.
- getPath() - Method in class NotFound
-
The path an object was not found at.
- getPath() - Method in class RootPath
-
A path on a file-system to the directory, that defines the root.
- getPath() - Method in class SingleFile
-
- getPath() - Method in class NamedFile
-
- getPath() - Method in class NamedPath
-
The path
- getPath() - Method in class RootedFilePath
-
- getPath() - Method in class StaticFilePath
-
- getPath() - Method in class FileDetails
-
- getPathAnnotation() - Method in class SinglePathStrategy
-
Derives the path to the corresponding annotation files, given a path to the image to be
annotated.
- getPathDefaultMarks() - Method in class MarkProposerStrategy
-
- getPathDictionary() - Method in class MarkProposerStrategy
-
- getPathLabel() - Method in class ImageCSVLabeller
-
Path to a CSV label file (comma-separated, with header, no quotes)
- getPathParser() - Method in class GroupFiles
-
- getPaths() - Method in class InputArguments
-
A list of paths referring to specific inputs;
- getPaths() - Method in class FileSetFromStringSet
-
- getPaths() - Method in class FilterForExistingFiles
-
All files need to be present
- getPayload() - Method in class TypedEdge
-
The edge.
- getPayload() - Method in class ObjectVertex
-
- getPenaltyValue() - Method in class MaxOverlapRatio
-
- getPeriodTriggerBank() - Method in class FeedbackBeginParameters
-
- getPermutation() - Method in class PermuteFeature
-
A permutation to apply.
- getPermutations() - Method in class PermuteFeature
-
A list of permutations to apply.
- getPermuteProperty() - Method in class Permute
-
- getPermuteProperty() - Method in class PermuteFeatureSequenceInteger
-
- getPixelsForPlane(int) - Method in class EncodedVoxels
-
- getPlotBackgroundColor() - Method in class PlotColorScheme
-
- getPlotGridlineColor() - Method in class PlotColorScheme
-
- getPlusOne() - Method in class SlidingBuffer
-
The voxel-buffer for the slice with the currently selected slice's index +1 or null
if it's the final slice.
- getPoint() - Method in class KernelPointCursor
-
The point around which the cursor may iterate.
- getPointFitters() - Method in class PointsInitialization
-
- getPoints() - Method in class PointListBase
-
- getPoints() - Method in class Contour
-
An ordered list of points in the contour.
- getPointsFitter() - Method in class CreateMarkFromPoints
-
- getPointsFitter() - Method in class MarkProposerStrategy
-
- getPointsFitter() - Method in class FitPoints
-
- getPointsFitter() - Method in class FitPointsFromObjects
-
- getPointsFitter() - Method in class PointsFitterToMark
-
- getPointsFitter() - Method in class ReflectInAxesWithinDistance
-
- getPointsFromOrientationProposer() - Method in class MergeLists
-
- getPointsFromOrientationXYProposer() - Method in class XYOrientationExtendToZ
-
- getPointsProposer() - Method in class FitPoints
-
- getPosition() - Method in class MarkWithPosition
-
- getPositionProposer() - Method in class Position
-
- getPositionProposer() - Method in class Repeat
-
- getPostcondition() - Method in class DilationContext
-
If defined, a condition which must be satisfied after an iteration occurs, otherwise
no more iterations occur.
- getPower() - Method in class MeanRaisedToPower
-
- getPredicates() - Method in class PathMatchConstraints
-
Predicates for both a file and a directory.
- getPrefix() - Method in class DefineAdderWithPrefixBean
-
A prefix that is placed before the name of every bean created.
- getPrefix() - Method in class PrependName
-
The string to prepend to the custom-name of each feature.
- getPrefix() - Method in class PathPrefixerAvoidResolve
-
A string prefixed to each output-path.
- getPrefix() - Method in class OutputterTarget
-
- getPrefix() - Method in class Outputter
-
- getPrefix() - Method in class OutputterChecked
-
- getPrefix() - Method in class DeriveFromPair
-
- getPrefix() - Method in class FeatureListProviderAggregatePair
-
The string to prepend.
- getPrefix() - Method in class ExperimentStructure
-
- getPrefixer() - Method in class OutputArguments
-
Where outputs are written, and how identifiers are styled.
- getPrefixer() - Method in class ParametersExperiment
-
- getPrefixer() - Method in class OutputManager
-
Determines a prefix to use when outputting a file based upon an input-path.
- getPrefixer() - Method in class PathPrefixerContext
-
Settings for where and how outputs should be prefixed.
- getPrefixer() - Method in class LastDirectoryAsPrefix
-
- getPrefixer() - Method in class Rooted
-
- getPrefixerElse() - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is not true.
- getPrefixerIf() - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is true.
- getPrefixToRemove() - Method in class DirectoryStructure
-
- getPrependColor() - Method in class Prepend
-
The color to prepend.
- getPriority() - Method in class PrioritisedVertex
-
- getProbNeg() - Method in class KernelPosNeg
-
- getProbPos() - Method in class KernelPosNeg
-
- getProgress() - Method in class InputManagerParameters
-
- getProperties() - Method in class ObjectWithProperties
-
A mapping between keys and corresponding values.
- getProperty(String) - Method in class ObjectWithProperties
-
Retrieves the value of a property corresponding to a particular name.
- getPropertyInitializer() - Method in class InitializableBean
-
Assigns a parameter, if possible, to a bean - as used by bean initializer.
- getPropertyPath() - Method in class PermuteProperty
-
Either a direct property of a bean or a nested-property with the children separated by
full-stops.
- getProposal() - Method in class OptimizationStep
-
- getProposal() - Method in class Reporting
-
- getProposalSecondary() - Method in class Reporting
-
An optional additional marks-Energy that provides an additional explanation of proposed
- getProposer() - Method in class MarkFromCollectionProposerUnary
-
- getProposer() - Method in class MarkProposerUnary
-
- getProvider() - Method in class FromProvider
-
- getPxlPartMemo() - Method in class FeatureInputAllMemo
-
- getPxlPartMemo() - Method in class FeatureInputSingleMemo
-
- getQuantile() - Method in class Quantile
-
The quantile.
- getQuantile() - Method in class QuantileStretch
-
- getQuantile() - Method in class Quantile
-
- getQuantile() - Method in class DiscardOutliers
-
- getQuantile() - Method in class Quantile
-
- getQuantile() - Method in class QuantileAcrossObjects
-
- getQuantile() - Method in class QuantileAcrossConnectedComponents
-
- getQuantileHigh() - Method in class Range
-
- getQuantileLow() - Method in class Range
-
- getQuantileLower() - Method in class ToByteUpperLowerQuantileIntensity
-
- getQuantileUpper() - Method in class ToByteUpperLowerQuantileIntensity
-
- getRadii() - Method in class Ellipse
-
- getRadii() - Method in class Ellipsoid
-
- getRadiiProposer() - Method in class OrientationAndRadiiProposer
-
- getRadiiProposer() - Method in class RadiiProposerRepeat
-
- getRadius() - Method in class MarkWithPositionAndSingleRadius
-
- getRadius() - Method in class AutoLocalThreshold
-
- getRadius() - Method in class WithRadiusBase
-
- getRadiusBound() - Method in class UniformRandomRadiiProposer
-
- getRadiusX() - Method in class FitResult
-
- getRadiusY() - Method in class FitResult
-
- getRadiusZ() - Method in class FitResult
-
- getRandomNumberGenerator() - Method in class ProposerContext
-
- getRangeAxisLimits() - Method in class PlotInstance
-
- getRangeC() - Method in class SizeExtents
-
- getRangeT() - Method in class SizeExtents
-
- getRangeZ() - Method in class SizeExtents
-
- getRate() - Method in class Geometry
-
- getRaw() - Method in class UnsignedByteBuffer
-
Gets an unsigned-byte (represented as a byte) at the current buffer position.
- getRaw(int) - Method in class UnsignedByteBuffer
-
Gets an unsigned-byte (represented as a byte) at a particular buffer position.
- getRaw() - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as an int) at the current buffer position.
- getRaw(int) - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as a int) at a particular buffer position.
- getRaw() - Method in class UnsignedShortBuffer
-
Gets an unsigned-short (represented as a short) at the current buffer position.
- getRaw(int) - Method in class UnsignedShortBuffer
-
Gets an unsigned-short (represented as a short) at a particular buffer position.
- getReader() - Method in class RotateImageToMatchEXIFOrientation
-
Reads the image that is subsequently flattened.
- getReaderMatching() - Method in class BranchExtension
-
The reader to use if the extension matches.
- getReaderNotMatching() - Method in class BranchExtension
-
The reader to use if the extension does not match.
- getReason() - Method in class NotFound
-
The reason an object could not be found.
- getReceive() - Method in class CombineBase
-
- getRecordedOutputs() - Method in class RecordedOutputsWithRules
-
If defined, records output-names that are written / not-written during the experiment.
- getRed() - Method in class RGBColorBean
-
The red component value of the RGB color.
- getRed() - Method in class RGBColor
-
The red component value of the RGB color.
- getRed() - Method in class ThreeChannels
-
- getReduce() - Method in class FeatureListProviderAggregatePair
-
Method for reducing all pairs into a single value e.g.
- getReferencePoissonIntensity() - Method in class MarkWithIdentifierFactory
-
- getReferences() - Method in class ReferencingFeatureListProvider
-
The names of other feature-lists, whose features may be referenced by this feature.
- getReferencesFeatureListCreator() - Method in class PermuteFeature
-
Makes sure a particular feature list creator is evaluated
- getReferencesList() - Method in class FeatureProviderReference
-
The name of the list in which the feature referenced by id resides.
- getRegex() - Method in class RegularExpressionBase
-
- getRegEx() - Method in class RegExMatcher
-
- getRegEx() - Method in class PathRegEx
-
Regular expression to use to match path with at least one group in it.
- getRegEx() - Method in class RemoveMatching
-
If a path matches a regular expression it is removed.
- getRegEx() - Method in class Exclude
-
A regular-expression to be matched against the identifiers of inputs.
- getRegEx() - Method in class InsertRegExGroups
-
The regular-expression to use for matching groups.
- getRegEx() - Method in class JoinRegExGroups
-
- getRegex() - Method in class Replace
-
Regular expression to match against string
- getRegex() - Method in class QuickBase
-
A regular-expression applied to the image file-path that matches three groups.
- getRegEx() - Method in class ExperimentStructure
-
- getRegexAdjacent() - Method in class NamedChannelsQuick
-
This needs to be set if there is at least one adjacentChannel.
- getRegExDir() - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to directories.
- getRegExFile() - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to files.
- getRegion() - Method in class Thresholded
-
- getRegion() - Method in class Intensity
-
- getRegionID() - Method in class RegionMembershipWithFlags
-
- getRegionID() - Method in class VolumeMin
-
- getRegionID() - Method in class FromMarks
-
- getRegionID() - Method in class IndexedRegionBase
-
- getRegionID() - Method in class ColoredMarks
-
- getRegionID() - Method in class FeatureMarkRegion
-
- getRegionID() - Method in class FeatureSingleMemoRegion
-
- getRegionID() - Method in class FeaturePairMemoSingleRegion
-
- getRegionID() - Method in class KernelBirthAndKill
-
- getRegionMap() - Method in class EnergySchemeCreatorByElement
-
- getRegionMap() - Method in class EnergyScheme
-
- getRegionMap() - Method in class EnergySchemeWithSharedFeatures
-
- getRegionMap() - Method in class EnergyMemoList
-
- getRegionMap() - Method in class VoxelizedMarkMemo
-
- getRegionMap() - Method in class ProposerContext
-
- getRegionMap() - Method in class FromMarks
-
- getRegionMap() - Method in class AsObject
-
- getRegionMap() - Method in class SurfaceSizeMaskNonZero
-
- getRegionMembership() - Method in class RegionMembershipWithFlags
-
- getRegularExpression() - Method in class TimestampPattern
-
The regular-expression that checks a match and specifies groups for the encoded date-time.
- getRejectionReason() - Method in class DualMarksAnnotation
-
A reason for rejection, if the annotation was rejected by the annotator.
- getRelation() - Method in class RelationToConstant
-
The relation to the threshold, where the threshold forms the second operand.
- getRelation() - Method in class ObjectFilterRelation
-
- getRelation() - Method in class MergePairs
-
Relation to threshold
- getRelation() - Method in class IdentityImposeValueRelationToHistogram
-
- getRelation() - Method in class RejectIfConditionXYResolution
-
A predicate defined by the relationship of the XY-resolution to a constant threshold.
- getRelation() - Method in class AddCriteriaFeatureRelationThreshold
-
- getRelation() - Method in class RequireFeatureRelationThreshold
-
- getRemainder() - Method in class SplitPath
-
The second component, what remains in the path.
- getRepeat() - Method in class MovieFromSlices
-
- getRepeats() - Method in class KernelBirth
-
Total number of births
- getRepeatZProvider() - Method in class GenerateString
-
Repeats the generated (2D) string in z, so it's the same z-extent as repeatZProvider
- getReplacement() - Method in class SubstituteRegularExpression
-
- getReplacement() - Method in class Replace
-
What to replace in the path
- getReplacement() - Method in class AdjacentFile
-
The replacement string used to determine the file
- getRequireArguments() - Method in class OnlyIf
-
The conditions that must be fulfilled
- getRequireArguments() - Method in class FeedbackReceiverRequireArguments
-
- getResizeTo() - Method in class GroupedMeanChannelTask
-
If set, each channel is scaled to a specific size before the mean is calculated (useful for
combining different sized images)
- getResizeTo() - Method in class HOGDescriptor
-
The input-image is rescaled to this width/height before calculating HOG descriptors
- getResizeTo() - Method in class HOGFeature
-
The input is rescaled to this width/height before calculating HOG descriptors.
- getResolution() - Method in class BinarySegmentationParameters
-
- getResolutionOptional() - Method in class FeatureInputDimensions
-
- getResolutionOptional() - Method in class FeatureInputEnergy
-
- getResolutionOptional() - Method in interface FeatureInputWithResolution
-
The resolution of the associated image, if it is available.
- getResolutionOptional() - Method in class FeatureInputHistogram
-
- getResolutionOptional() - Method in class FeatureInputMarkCollection
-
- getResolutionOptional() - Method in class FeatureInputMark
-
- getResolutionRequired() - Method in interface FeatureInputWithResolution
-
The resolution of the associated image, or an exception if it is not available.
- getRestrictTo() - Method in class Invert
-
If set, the inversion only occurs on a particular region of the mask, as determined by this
mask
- getResult(int) - Method in class ResultsVector
-
Gets a result value at a particular position.
- getResults() - Method in class FeatureInputResults
-
The results of a prior feature-calculation, corresponding to a list of features.
- getResults() - Method in class LabelledResultsVector
-
The results.
- getResults() - Method in class FeatureCalculationContext
-
The stored results and thumbnail writer.
- getResults() - Method in class FeatureExporter
-
Saved store feature calculation results, and writes associated thumbnails.
- getResults() - Method in class LabelledResultsVectorWithThumbnail
-
The results.
- getResultsVector() - Method in class ResultsVectorWithThumbnail
-
- getRGB() - Method in class RGBColorBean
-
- getRGB() - Method in class RGBColor
-
- getRgb() - Method in class StackWriteAttributes
-
Whether it's an RGB or RGBA image when it has three/four channels respectively.
- getRight() - Method in class ObjectsToCompare
-
Objects on right-side of the comparison
- getRightUnassigned() - Method in class OverlappingObjects
-
The unassigned objects in the right set.
- getRoot() - Method in class SplitPath
-
The first component, the root of the path.
- getRoot() - Method in class ProposerFailureDescription
-
- getRoot() - Method in class TestLoader
-
Path to where the test-data is stored.
- getRoot1() - Method in class QuadraticEquationSolver.QuadraticRoots
-
The first root.
- getRoot2() - Method in class QuadraticEquationSolver.QuadraticRoots
-
The second root.
- getRootDirectory() - Method in class Manifest
-
- getRootName() - Method in class Rooted
-
The name of the root-path to associate with this fileset.
- getRootName() - Method in class RootedFilePath
-
- getRootName() - Method in class Rooted
-
- getRootName() - Method in class Rooted
-
- getRootName() - Method in class QuickBase
-
If non-empty then a rooted filesystem is used with this root
- getRootName() - Method in class RootedExperiment
-
Root-name assuming multi-rooted structure.
- getRootNameForStructure() - Method in class ExperimentResultsExperimentStructure
-
If rootInStructure==true, the rootName is placed in the folder structure.
- getRootPath() - Method in class DeserializedManifest
-
- getRotationAngle() - Method in class BoundRotation2D
-
- getRotationMatrix() - Method in class Orientation
-
Derives a
RotationMatrix that can be applied to rotate an entity
anti-clockwise to the current orientation.
- getRotationMatrix() - Method in class OrientationRotationMatrix
-
The rotation-matrix.
- getRotationX() - Method in class BoundRotation3D
-
- getRotationY() - Method in class BoundRotation3D
-
- getRotationZ() - Method in class BoundRotation3D
-
- getRotMatrix() - Method in class FitResult
-
The rotation matrix, which must be considered immutable to be used here.
- getRow(int) - Method in class TableItemArrangement
-
- getRow() - Method in class Cell
-
- getRowForListIndex(int) - Method in class TableItemArrangement
-
- getRunningSum() - Method in class RunningSumParented
-
- getSampleEvery() - Method in class SampleWithDirectory
-
- getScalarProposer() - Method in class MaxWithConstant
-
- getScalarProposer() - Method in class Scale
-
- getScale() - Method in class MeanScale
-
The scale, typically the standard-deviation.
- getScale() - Method in class MontageSlices
-
Whether to increase or reduce the size of the images
- getScaleCalculator() - Method in class ScaleXY
-
- getScaleCalculator() - Method in class ScaleXY
-
Determines how much to scale by
- getScaleCalculator() - Method in class Scale
-
- getScaleCalculator() - Method in class AtScale
-
- getScaleCalculator() - Method in class Invert
-
- getScaleCalculator() - Method in class ScaleImage
-
Calculates what scale-factor to apply on the image.
- getScaleCalculator() - Method in class ScaleXY
-
- getScaleFactor() - Method in class GradientBase
-
- getScaleLower() - Method in class ScaleByDictionary
-
- getScaleLower() - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the min by multiplying the quantileLower by this constant.
- getScaleRadii() - Method in class ConicFitterBase
-
- getScaleUpper() - Method in class ScaleByDictionary
-
- getScaleUpper() - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the max by multiplying the quantileUpper by this constant.
- getScore() - Method in class ScoreVoxels
-
- getScoreExtracter() - Method in class AcceptanceProbabilityCalculator
-
- getScoreProvider() - Method in class ExtractSlice
-
- getSearchObjects() - Method in class FeatureIntersectingObjects
-
- getSecond() - Method in class CostMatrix
-
The second set of elements.
- getSecond() - Method in class FeatureInputPairObjects
-
- getSecond() - Method in class OutputEnableRulesSpecify
-
Output-names in the second-level (for all first level output-names)
- getSecond() - Method in class Compose
-
Second transformation from U to T
- getSecondary() - Method in class StateReporterToPixelized
-
- getSegment() - Method in class BinarySegmentationOne
-
- getSegment() - Method in class SegmentChannelIntoObjectsUnary
-
- getSegment() - Method in class SegmentChannel
-
Segmentation algorithm
- getSegment() - Method in class SegmentChannel
-
- getSegment() - Method in class SegmentChannelByObject
-
- getSegment() - Method in class SegmentStack
-
The segmentation procedure.
- getSegment() - Method in class SegmentWithSeeds
-
- getSegment() - Method in class ConnectedComponentsFromBinarySegmentation
-
- getSegment() - Method in class SegmentInstanceWithModel
-
The segmentation algorithm.
- getSegment() - Method in class SegmentMarksFromImage
-
How to perform the segmentation.
- getSegmentStack() - Method in class SegmentOnMaximumIntensityAndExpandInZ
-
- getSelect() - Method in class DeriveFromPair
-
Either "merged" or "first" or "second" indicating which feature to delegate from
- getSelectChannels() - Method in class GroupedStackBase
-
Selects which channels are included, optionally renaming.
- getSemiMajorAxis() - Method in class EllipseStandardFormConverter
-
- getSemiMinorAxis() - Method in class EllipseStandardFormConverter
-
- getSeperator() - Method in class CombineCSV
-
- getSequence() - Method in class PermutePropertySequence
-
A sequence of integers, with each element assigned assigned directly during the permutation,
or after further manipulation.
- getSequence() - Method in class ChangeableOutputSequence
-
- getSequenceType() - Method in class OutputSequenceIndexed
-
- getSequenceType() - Method in class ManifestDirectoryDescription
-
A sequence-type to describe the different filenames outputted in the directory.
- getSeriesColors() - Method in class PlotIndexBaseCategorical
-
- getSeriesIndex() - Method in class FromStackReader
-
The series to open to the read the metadata (zero-indexed).
- getSeriesNameFor(int) - Method in class PlotIndexBase
-
- getSettings() - Method in class Outputter
-
- getSettings() - Method in class OutputterChecked
-
General settings for outputting.
- getSettings() - Method in class OutputWriteContext
-
User-define settings for outputting in output-manager.
- getSettings() - Method in class ElementOutputter
-
General settings for outputting.
- getSharedFeatures() - Method in class FeatureRelatedInitialization
-
Shared features available for reference during calculation.
- getSharedFeatures() - Method in class EnergySchemeSet
-
- getSharedFeatures() - Method in class EnergySchemeWithSharedFeatures
-
- getSharedObjects() - Method in class FeatureInitialization
-
Shared-objects, which can be referenced by the feature to influence calculation.
- getSharedObjects() - Method in class ImageInitialization
-
- getSharedState() - Method in class InputBound
-
- getSharedState() - Method in class ParametersUnbound
-
- getSharedState() - Method in class CopyContext
-
State shared across all inputs when copying.
- getSharedState() - Method in class SharedStateRememberConverted
-
The shared state.
- getShell() - Method in class MarkEllipseFactory
-
- getShell() - Method in class MarkEllipsoidFactory
-
- getShell() - Method in class Ellipse
-
The size of the shell, expressed as a ratio of the radius.
- getShell() - Method in class Ellipsoid
-
- getShell() - Method in class FromObjects
-
- getShell() - Method in class CreateEllipse
-
- getShell() - Method in class ConicFitterBase
-
- getShortTitle() - Method in class Plot
-
- getShowOngoingJobsLessThan() - Method in class ParallelProcessor
-
When the number of ongoing jobs is less than this threshold, they are shown in event logs.
- getSigma() - Method in class BlurStrategy
-
- getSigma() - Method in class GaussianBlur2D
-
- getSimplePairCollectionID() - Method in class KernelMerge
-
- getSingle() - Method in class MergedPairsFeatures
-
- getSize() - Method in class TaskArguments
-
Suggests dimensions or a scaling-factor to resize an image to.
- getSize() - Method in class TextStyle
-
Explicit size of the image the string is draw on
- getSize() - Method in class Kernel
-
The size of the kernel-matrix in one dimension, either X or Y.
- getSize() - Method in class Aggregator
-
- getSize() - Method in class PlotHistogram
-
Size of the image produced showing a plot of the histogram.
- getSize() - Method in class OutlinePreserveRelativeSize
-
Size of all created thumbnails
- getSize() - Method in class ScaleToSize
-
- getSize() - Method in class MovieFromSlices
-
- getSize() - Method in class IntegerRange
-
- getSizeXY() - Method in class SpecifyDimensions
-
Length of X and Y dimensions.
- getSizeZ() - Method in class SpecifyDimensions
-
Length of Z dimension.
- getSkipFirstTrim() - Method in class RemoveTrailingDirectory
-
- getSkipFirstTrim() - Method in class FilePathAppendBase
-
- getSkipNumberSubdirectories() - Method in class LastDirectories
-
Initially skip this number of directories before including them in the description.
- getSlice(int) - Method in interface VoxelPartition
-
- getSlice(int) - Method in class VoxelPartitionHistogram
-
- getSlice() - Method in class RepeatSlice
-
- getSliceFirst() - Method in class MontageSlices
-
First slice.
- getSliceID() - Method in class SelectSlicesBase
-
Index of slice to use, or -1 to use all slices
- getSliceIndex() - Method in class RepeatSlice
-
Which slice to use from mask
- getSliceIndex() - Method in class FileDetails
-
- getSliceLast() - Method in class MontageSlices
-
Last slice.
- getSmoothingFactor() - Method in class SplitContourAtSaddlePoints
-
- getSource() - Method in class StringMapItem
-
The origin of the mapping.
- getSource() - Method in class MatchedObject
-
The source object (which is matched against others)
- getSource() - Method in class IdentifiablePair
-
- getSource() - Method in class PairPxlMarkMemo
-
- getSource() - Method in class ExportFeatures
-
Source of feature-values to be exported.
- getSource() - Method in class DualVoxelizedMarks
-
- getSource() - Method in class ToVoxelized
-
- getSourceDirectory() - Method in class CopyContext
-
Source directory of copying.
- getSources() - Method in class MultipleComparer
-
The other entities to compare with the annotation.
- getSplitIdentifierRegex() - Method in class CompareAnnotations
-
If non-empty, the string (a regular-expression) is used to split the file's identifier into
groups.
- getSplitProposer() - Method in class KernelSplit
-
- getSquareSize() - Method in class SplitIntoSquares
-
- getStack() - Method in class StackProviderUnary
-
- getStack() - Method in class DisplayStack
-
The underlying stack that will be displayed, possibly after conversion.
- getStack() - Method in class StackProviderWithLabel
-
- getStack() - Method in class ColoredMarksWithDisplayStack
-
- getStack() - Method in class MarksWithDisplayStack
-
- getStack() - Method in class FromStack
-
Provides a stack.
- getStack() - Method in class SegmentStack
-
The stack to segment
- getStack() - Method in class ExportObjectsFromCSV
-
The stack that is the background for our objects
- getStackEnergy() - Method in class FeatureEvaluator
-
Optionally specifies an energy-stack to be associated with every calculation input.
- getStackEnergy() - Method in class FromImage
-
Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is
considered to be the input stacks).
- getStackEnergy() - Method in class BinaryClassifierImageLabeller
-
- getStackEnergy() - Method in class ExtractSlice
-
- getStackEnergy() - Method in class DefineOutputterWithEnergy
-
- getStackID() - Method in class IfStackExists
-
- getStackName() - Method in class One
-
If defined, processing only occurs the stack with this specific stack and index.
- getStackNameDefault() - Method in class AnnotationBackground
-
The name of the default stack from backgroundStackMap to display as background when
annotating.
- getStackProviderID() - Method in class FromStack
-
Specifies the ID of an existing stack.
- getStackProviderID() - Method in class FromStackChannel
-
- getStackReader() - Method in class AnnotatorStrategy
-
How to read raster
Stacks from the file-system.
- getStackReader() - Method in class InputManagerWithStackReader
-
- getStackReader() - Method in class MaskAsObject
-
How to read the
Mask from the file-system.
- getStackReader() - Method in class AnnotationComparisonInput
-
- getStackReader() - Method in class FromStackReader
-
- getStackReader() - Method in class FlattenAsChannel
-
Reads the image that is subsequently flattened.
- getStackReader() - Method in class ImposeResolution
-
Reads an image before a resolution is imposed.
- getStackReader() - Method in class MultiFileReader
-
- getStackReader() - Method in class ReadVoxelExtentXml
-
Reads an image before a resolution is imposed.
- getStackReader() - Method in class RejectIfConditionXYResolution
-
Reads an image before a resolution is imposed.
- getStackReaderAdjacent() - Method in class NamedChannelsQuick
-
The raster-reader to use for opening any adjacent-channels
- getStackReaderAppend() - Method in class QuickBase
-
The raster-reader for reading any appended files
- getStackStore() - Method in class ChannelSource
-
- getStart() - Method in class SequenceInteger
-
The index to begin iteration from.
- getStartIndex() - Method in class IndexRangeNegative
-
The index if the first element to use in the subsetting range, zero-indexed.
- getStartIndex() - Method in class MovieFromSlices
-
- getStartingIntensity() - Method in class FloodFillEachIntensityLevel
-
The first intensity-value to consider as a valid object (e.g.
- getStartPoint() - Method in class LineSegment
-
- getState() - Method in class FeedbackEndParameters
-
- getStateReporter() - Method in class TransformationAssignMode
-
- getStrategy() - Method in class AnnotationWithStrategy
-
The strategy on how annotation occurs.
- getStrategy() - Method in class BoundReplaceStrategy
-
- getStrategy() - Method in class Blur
-
- getStringRasterGenerator() - Method in class GenerateString
-
- getStyle() - Method in class ExportFeatures
-
Visual style for how feature export occurs.
- getStyle() - Method in class SegmentInstanceWithModel
-
Visual style for how feature export occurs.
- getSubdirectory() - Method in class AppendDictionary
-
- getSubdirectory() - Method in class ExperimentResultsExperimentStructure
-
If non-empty than an additional subdirectory is appended as a suffix
${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
- getSubdirectoryName() - Method in class OutputPattern
-
The name of a subdirectory in the current context to write to, or if empty, files are written
into the current directory context.
- getSubtractConstant() - Method in class IntensityGradientBase
-
- getSubtractRadii() - Method in class ConicFitterBase
-
- getSuggestedFormatToWrite() - Method in class StackWriteOptions
-
A suggestion on what file-format to write.
- getSuggestedFormatToWrite() - Method in class OutputWriteContext
-
A suggestion on what file-format to write.
- getSuggestedFormatToWrite() - Method in class ElementOutputter
-
- getSuggestedImageOutputFormat() - Method in class OutputPrefixerSettings
-
A file format suggested for writing images to the file system.
- getSuggestedResize() - Method in class InitializationContext
-
A suggested input on how to resize an image, if one is provided.
- getSuggestedResize() - Method in class ImageInitialization
-
- getSum() - Method in class RunningSum
-
The running sum.
- getSummarizer() - Method in class SummarizerInputFromManager
-
- getSummarizer() - Method in class SummarizeBase
-
- getSummarizerElse() - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) <= countThreshold
- getSummarizerGreaterThan() - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) > countThreshold
- getTarget() - Method in class StringMapItem
-
The destination of the mapping.
- getTargetClass() - Method in class ExtractDerivedParameter
-
The class of the target type T.
- getTargetSize() - Method in class FitTo
-
The target size.
- getTask() - Method in class JobProcessor
-
- getTask() - Method in class ExperimentExecutor
-
- getTask() - Method in class ConvertNamedChannels
-
The underlying task that will be called, perhaps with a different input-type.
- getTask() - Method in class QuickExperiment
-
- getTask() - Method in class QuickMultiDatasetExperiment
-
- getTask() - Method in class QuickMultiDatasetStructuredExperiment
-
- getTaskArguments() - Method in class InputBound
-
- getTaskName() - Method in class TaskArguments
-
A name to describe the ongoing task.
- getTaskProcessor() - Method in class InputOutputExperiment
-
What task is associated with the experiment, and how it is processed.
- getTemperature() - Method in class Aggregator
-
- getTemperature() - Method in class Reporting
-
- getTemplateMark() - Method in class MarkWithIdentifierFactory
-
- getTemporary() - Method in class EncodedVoxels
-
- getTermination() - Method in class SimulatedAnnealing
-
- getText() - Method in class GenerateString
-
Text to draw on an image
- getThreshold() - Method in class RelationToConstant
-
The constant threshold.
- getThreshold() - Method in class CutBelowThreshold
-
- getThreshold() - Method in class CalculateLevelRelativeToThreshold
-
- getThreshold() - Method in class IntensityGreaterEqualThan
-
- getThreshold() - Method in class ThresholdedFeature
-
- getThreshold() - Method in class ThresholdedVolume
-
- getThreshold() - Method in class Count
-
- getThreshold() - Method in class RatioThreshold
-
- getThreshold() - Method in class FeatureIntersectingObjectsThreshold
-
Only considers values greater or equal to the threshold
- getThreshold() - Method in class AddCriteriaFeatureRelationThreshold
-
- getThreshold() - Method in class RequireFeatureRelationThreshold
-
- getThreshold() - Method in class GreatestAreaSlice
-
- getThreshold() - Method in class Thresholded
-
- getThreshold() - Method in class IfCondition
-
- getThresholder() - Method in class BinarySegmentationThreshold
-
- getThresholder() - Method in class Threshold
-
The thresholder that will convert a channel into a binary-channel
- getThresholdHours() - Method in class ClusterByTimestamp
-
Files whose creation-time differs <= this parameter are joined into the same cluster.
- getThresholdNumberObjectsGlobal() - Method in class ThresholdConfidence
-
When the number of objects is greater or equal than this, they are reduced globally, without
separation.
- getThumbnail() - Method in class CombineObjectsForFeatures
-
Generates a thumbnail representation of one or more combined objects, as form a single input.
- getThumbnail() - Method in class FromImage
-
Method to generate a thumbnail for images.
- getThumbnail() - Method in class ResultsVectorWithThumbnail
-
- getThumbnailBatch() - Method in class ListWithThumbnails
-
- getTime() - Method in class JobState
-
- getTimeAnnotationLastUpdated() - Method in class DualMarksAnnotation
-
Number of seconds since the UNIX epoch
- getTimeIndex() - Method in class ConvertNamedChannelsToStack
-
- getTimeIndex() - Method in class FileDetails
-
- getTimeIndexGroupID() - Method in class RegularExpression
-
- getTimes() - Method in class Repeat
-
How many times to duplicate the list.
- getTimestampPatterns() - Method in class ClusterByTimestamp
-
The patterns which can be used to extract a date-time from a filename.
- getTimeZoneOffset() - Method in class ClusterByTimestamp
-
If >= 0, sets a specific time-offset in hours.
- getTitle() - Method in class ReportFeatureEvaluator
-
- getTitle() - Method in class Plot
-
The full title of the plot.
- getTitle() - Method in class ReportFeatureForManifestFileBase
-
- getTo() - Method in class TypedEdge
-
The vertex the edge joins to.
- getTolerance() - Method in class UnchangedScore
-
An exponent of 10 which determines a tolerance, less than which a score will be deemed
unchanged compared to another.
- getTotal() - Method in class EnergyTotal
-
- getTotalCount() - Method in class Histogram
-
The total count across values in the histogram.
- getTotalNumberTasks() - Method in class ConcurrentJobMonitor
-
- getTransformer() - Method in class RemovePartitionAndThen
-
- getTransformer() - Method in class VoxelizeWithTransform
-
- getTransformer() - Method in class KernelStateBridgePixelize
-
- getTransformerKernelToState() - Method in class KernelStateBridgeTransformer
-
- getTransformerMarks() - Method in class AddDualTransformer
-
- getTransformerPrimary() - Method in class StateReporterTransformer
-
- getTransformerSecondary() - Method in class StateReporterTransformer
-
- getTransformerStateToKernel() - Method in class KernelStateBridgeTransformer
-
- getTriggerTerminationCondition() - Method in class OptimizationContext
-
- getTrimTrailingDirectory() - Method in class RemoveTrailingDirectory
-
- getTrimTrailingDirectory() - Method in class FilePathAppendBase
-
- getType() - Method in class ManifestDescription
-
Identifies the type of entity.
- getUnconvertedVoxelAt(int, Point3i) - Method in class DisplayStack
-
Retrieve the intensity of a voxel at a particular point, before any conversion is applied.
- getUniqueLabel() - Method in class AnnotationLabel
-
Label that uniquely identifies the ID (for machine purposes)
- getUnit() - Method in class BoundingBoxExtent
-
- getUnit() - Method in class FeatureSingleMemoRegion
-
- getUnitConverterOptional() - Method in class FeatureInputEnergy
-
Converts voxelized measurements to/from physical units.
- getUnitType() - Method in class DistancePhysical
-
- getUnitType() - Method in class AreaPhysical
-
- getUnitType() - Method in class VolumePhysical
-
- getUnitType() - Method in class FeatureConvertUnits
-
- getUnitType() - Method in class UnitConverter
-
- getUnitTypeFrom() - Method in class ConvertUnits
-
- getUnitTypeTo() - Method in class ConvertUnits
-
- getUnitValueDistance() - Method in class FromUnitValueDistance
-
- getUnsigned() - Method in class UnsignedBufferAsInt
-
Gets an unsigned-byte (represented as a int) at the current buffer position.
- getUnsigned(int) - Method in class UnsignedBufferAsInt
-
Gets an unsigned-byte (represented as a int) at a particular buffer position.
- getUnsigned() - Method in class UnsignedByteBuffer
-
- getUnsigned(int) - Method in class UnsignedByteBuffer
-
- getUnsigned() - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as a long) at the current buffer position.
- getUnsigned(int) - Method in class UnsignedIntBuffer
-
Gets an unsigned-int (represented as a long) at a particular buffer position.
- getUnsigned() - Method in class UnsignedShortBuffer
-
- getUnsigned(int) - Method in class UnsignedShortBuffer
-
- getUnsignedByte() - Static method in class VoxelsFactory
-
A factory that creates voxels of type unsigned byte.
- getUnsignedInt() - Static method in class VoxelsFactory
-
A factory that creates voxels of type unsigned int.
- getUnsignedShort() - Static method in class VoxelsFactory
-
A factory that creates voxels of type unsigned short.
- getUserFriendlyLabel() - Method in class AnnotationLabel
-
Descriptive user-friendly label displayed via GUI
- getValue() - Method in class NamedBean
-
- getValue() - Method in interface NameValue
-
The associated value.
- getValue() - Method in class SimpleNameValue
-
- getValue() - Method in class TypedValue
-
The value.
- getValue() - Method in class Constant
-
The constant value.
- getValue() - Method in class DistancePhysical
-
- getValue() - Method in class DistanceVoxels
-
- getValue() - Method in class UnitValueArea
-
- getValue() - Method in class VolumePhysical
-
- getValue() - Method in class VolumeVoxels
-
- getValue() - Method in class OptionalNameValue
-
The value.
- getValue() - Method in class AssignValue
-
- getValue() - Method in class CreateNew
-
- getValue() - Method in class UnaryWithValueBase
-
- getValue() - Method in class DictionaryCondition
-
The value the key should have in the dictionary, in order for the condition to be fulfilled.
- getValue() - Method in class EmptyHistogramConstant
-
- getValue() - Method in class IfParamEqual
-
- getValue() - Method in class ConstantScaleFactor
-
- getValue() - Method in class CountEqual
-
- getValue() - Method in class IdentityImposeValueRelationToHistogram
-
- getValue() - Method in class NormalizeByConstant
-
- getValue() - Method in class Constant
-
- getValue() - Method in class Constant
-
- getValue() - Method in class WithValueBase
-
- getValueIfEmpty() - Method in class FeatureHistogramStatistic
-
The value to return iff exceptionifEmpty is false.
- getValueIfTooFewVoxels() - Method in class ImageMomentsBase
-
A value to return if there are too few voxels (less than MIN_NUM_VOXELS to calculate
moments
- getValueNoObject() - Method in class ScoreObjects
-
- getValueNoObjects() - Method in class FeatureIntersectingObjects
-
- getValues() - Method in class StatisticsToExport
-
- getValues() - Method in class PermutePropertyDoubleSet
-
The respect double values to assign during the permutation.
- getValues() - Method in class PermutePropertyStringSet
-
The respect string values to assign during the permutation.
- getVersion() - Method in class ExperimentIdentifierConstant
-
- getVertex() - Method in class PrioritisedVertex
-
- getVerticalAlign() - Method in class Overlay
-
- getVisitScheduler() - Method in class TraverseOuterContourOnImage
-
- getVoxelDataType() - Method in class Channel
-
The underlying data-type of the voxels in the channel, represented by a
VoxelDataType
instance.
- getVoxelDataType() - Method in class VoxelsUntyped
-
The underlying data-type of the voxels, represented by a
VoxelDataType instance.
- getVoxels() - Method in class SlidingBuffer
-
The voxels from which buffers corresponding to slices are extracted.
- getVoxelsConverter() - Method in class MaxIntensity
-
- getVoxelsConverter() - Method in interface ChannelConverterAttached
-
Converts voxels to have type voxel-type T.
- getVoxelsConverter() - Method in class MaxIntensityFromHistogram
-
- getVoxelsConverter() - Method in class QuantileIntensityFromHistogram
-
- getVoxelsConverter() - Method in class UpperLowerQuantileIntensityFromHistogram
-
- getVoxelsConverter() - Method in class ChannelConverter
-
A converter used to change the
Voxels to
targetDataType.
- getWeight() - Method in class WeightedKernel
-
- getWeight() - Method in class KernelProposerOptionSingle
-
- getWeightBackground() - Method in class OtsuWeighted
-
- getWeightedKernelFactory(int) - Method in class KernelProposer
-
- getWeightForeground() - Method in class OtsuWeighted
-
- getWeightItem1Greater() - Method in class Range
-
- getWeightItem2Greater() - Method in class Range
-
- getWeightNegative() - Method in class KernelProposerOption
-
- getWeightNegative() - Method in class KernelProposerOptionDual
-
- getWeightNegative() - Method in class KernelProposerOptionSingle
-
- getWeightPositive() - Method in class KernelProposerOption
-
- getWeightPositive() - Method in class KernelProposerOptionDual
-
- getWeightPositive() - Method in class KernelProposerOptionSingle
-
- getWeightWidthDescription() - Method in class ImageLabelStrategy
-
- getWhenBinaryChannel() - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled binary image.
- getWhenDetailed() - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is on
- getWhenEqual() - Method in class IfParamEqual
-
- getWhenFalse() - Method in class IfElse
-
- getWhenNot() - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is off
- getWhenNotEightBit() - Method in class BranchChannels
-
Writer employed if a stack contains channels that are not 8-bit.
- getWhenNotEqual() - Method in class IfParamEqual
-
- getWhenRelative() - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is selected.
- getWhenRGB() - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled RGB image.
- getWhenRGBAlpha() - Method in class BranchChannels
-
Writer employed if a stack is a four-channeled RGBA image.
- getWhenSingleChannel() - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
- getWhenThreeChannels() - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled non-RGB image.
- getWhenTrue() - Method in class IfElse
-
- getWidth() - Method in class SizeXY
-
Size in X dimension.
- getWidth() - Method in class Difference
-
Width (what the difference is divided by)
- getWidth() - Method in class ImposeResolution
-
Physical pixel size of a voxel in x-dimension.
- getWidthFactor() - Method in class DifferenceCalculateLevelStandardDeviation
-
- getWindowSize() - Method in class CenterSliceWindow
-
- getWindowSize() - Method in class HOGParameters
-
The window-size as per OpenCV implementation.
- getWithin() - Method in class UnitsWithinRange
-
Returned as a constant if a value lies within the range
- getWithinValue() - Method in class CompareWithRange
-
Constant to return if value lies within the range
- getWithinValue() - Method in class CompareWithRangeFeature
-
Constant to return if value lies within the range
- getWriter() - Method in class Flatten
-
- getWriter() - Method in class TextFileOutput
-
- getWriter() - Method in class BranchChannels
-
Default writer, if a more specific writer is not specified for a condition.
- getWriter() - Method in class WriteResolutionXml
-
- getWriterAlways2D() - Method in class BranchStack
-
Writer to use if it is guaranteed that the image will always be 2D.
- getWriterElse() - Method in class BranchStack
-
Otherwise the writer to use.
- getWriterIfNoSuggestion() - Method in class BranchSuggestedFormat
-
The writer to use if there is no suggested file-format.
- getWriterInstance(Class<? extends T>) - Method in class OutputWriteSettings
-
Gets a writer-instance for a particular writerParentClass.
- getWriters() - Method in class OutputWriteSettings
-
Specifies a writer bean instance for a particular type of writer (identified by the writer
bean class)
- getWriters() - Method in class OutputterChecked
-
The writers associated with this output-manager.
- getWritersIfSuggested() - Method in class BranchSuggestedFormat
-
A list of writers to select if a given format is used
- getX() - Method in class VectorInDirection
-
- getX() - Method in class PlotAxisLabels
-
- getXDiv() - Method in class Orientation
-
- getXmlAggregatedGroup() - Method in class FeatureOutputNames
-
The name of the XML file outputted with aggregated values for each group, if enabled.
- getXMLConfiguration() - Method in class Experiment
-
- getY() - Method in class VectorInDirection
-
- getY() - Method in class PlotAxisLabels
-
- getYAxisLowerMargin() - Method in class LinePlot
-
- getYAxisUpperMargin() - Method in class LinePlot
-
- getYVal(T, int) - Method in interface LinePlot.YValGetter
-
- getYValGetter() - Method in class BarPlot
-
- getYValGetter() - Method in class LinePlot
-
- getZ() - Method in class VectorInDirection
-
- getZAlign() - Method in class Overlay
-
- getZSliceGroupID() - Method in class RegularExpression
-
- getZSliceNum() - Method in class SortedSetSlice
-
- GlobalRegionIdentifiers - Class in org.anchoranalysis.mpp.mark
-
- GlobExtractor - Class in org.anchoranalysis.io.input.path
-
Extracts a glob from a string describing it, and a direcory which gives it context.
- GlobExtractor.GlobWithDirectory - Class in org.anchoranalysis.io.input.path
-
- GlobWithDirectory(Optional<String>, String) - Constructor for class GlobExtractor.GlobWithDirectory
-
- GradientBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Base class to calculate the gradient of the voxels in a
Channel.
- GradientBase() - Constructor for class GradientBase
-
- GradientBaseAddSum - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Like
GradientBase but allows an arbitrary constant to be added to voxels storing the
gradient.
- GradientBaseAddSum() - Constructor for class GradientBaseAddSum
-
- gradientCalculation() - Method in class IntensityGradientBase
-
- GradientForAxis - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Extracts the gradient in the direction of a particular axis (identified by an index)
- GradientForAxis() - Constructor for class GradientForAxis
-
- GradientMagnitude - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular
direction
- GradientMagnitude() - Constructor for class GradientMagnitude
-
- GradientMeanForAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular
direction
- GradientMeanForAxis() - Constructor for class GradientMeanForAxis
-
- GradientXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Calculates a
Channel's gradient along the x and y axes.
- GradientXY() - Constructor for class GradientXY
-
- GraphLogger - Class in org.anchoranalysis.plugin.image.object.merge
-
- GraphLogger(DescribeGraph, Logger) - Constructor for class GraphLogger
-
- GraphWithoutPayload<V> - Class in org.anchoranalysis.core.graph
-
A graph, either directed or undirected, where edges contain no payload.
- GraphWithoutPayload(boolean) - Constructor for class GraphWithoutPayload
-
Creates the graph.
- GraphWithPayload<V,P> - Class in org.anchoranalysis.core.graph
-
A graph, either directed or undirected, with edges containing a payload of type E.
- GraphWithPayload(boolean) - Constructor for class GraphWithPayload
-
Creates the graph.
- GrayscaleReconstruction2DIJ - Class in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
-
- GrayscaleReconstruction2DIJ() - Constructor for class GrayscaleReconstruction2DIJ
-
- GrayscaleReconstructionByErosion - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
-
- GrayscaleReconstructionByErosion() - Constructor for class GrayscaleReconstructionByErosion
-
- GrayscaleReconstructionRobinson - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
-
- GrayscaleReconstructionRobinson() - Constructor for class GrayscaleReconstructionRobinson
-
- GreaterIntersectionWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Only accepts an object if it has greater (or EQUAL) intersection with objectsGreater than
objectsLesser
- GreaterIntersectionWith() - Constructor for class GreaterIntersectionWith
-
- GreaterThan - Class in org.anchoranalysis.math.relation
-
Returns true iff valueFirst is greater than valueSecond.
- GreaterThan() - Constructor for class GreaterThan
-
- GreaterThanBean - Class in org.anchoranalysis.bean.shared.relation
-
A relation double1 > double2.
- GreaterThanBean() - Constructor for class GreaterThanBean
-
- GreaterThanEqualTo - Class in org.anchoranalysis.math.relation
-
Returns true iff valueFirst is greater than or equal to valueSecond.
- GreaterThanEqualTo() - Constructor for class GreaterThanEqualTo
-
- GreaterThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation
-
A relation double1 >= double2.
- GreaterThanEqualToBean() - Constructor for class GreaterThanEqualToBean
-
- GreaterThanThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
-
Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the
threshold
- GreaterThanThreshold() - Constructor for class GreaterThanThreshold
-
- GreatestAreaSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- GreatestAreaSlice() - Constructor for class GreatestAreaSlice
-
- greedyMatch() - Method in class HungarianAlgorithm
-
Find a valid matching by greedily selecting among zero-cost matchings.
- GREEN - Static variable in class RGBChannelNames
-
Name for the green channel.
- green() - Method in class RGBStack
-
The green channel.
- GroupedAnnotationLabels - Class in org.anchoranalysis.plugin.annotation.bean.label
-
A set of annotation labels partitoned into their unique groups
- GroupedAnnotationLabels(Collection<AnnotationLabel>) - Constructor for class GroupedAnnotationLabels
-
- groupedLabels() - Method in class ImageLabelStrategy
-
- GroupedMeanChannelTask - Class in org.anchoranalysis.plugin.image.task.bean.grouped.raster
-
Creates a an aggregated-image for each group, where each voxel-value is the mean voxel-value
across the group.
- GroupedMeanChannelTask() - Constructor for class GroupedMeanChannelTask
-
- GroupedResults - Class in org.anchoranalysis.feature.io.results.group
-
Stores feature-calculation results, indexing by their group.
- GroupedResults() - Constructor for class GroupedResults
-
- GroupedSharedState<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped
-
Commonality between shared state for gouped export tasks
- GroupedSharedState(Function<ConsistentChannelChecker, GroupMapByName<S, T>>) - Constructor for class GroupedSharedState
-
- GroupedStackBase<S,T> - Class in org.anchoranalysis.plugin.image.task.bean.grouped
-
Base class for stacks (usually each channel from an image) that are somehow grouped-together.
- GroupedStackBase() - Constructor for class GroupedStackBase
-
- GroupFiles - Class in org.anchoranalysis.plugin.io.bean.file.group
-
- GroupFiles() - Constructor for class GroupFiles
-
- groupForKey(String) - Method in class AnnotationComparisonAssigner
-
- groupForKey(String) - Method in class FeatureCostAssigner
-
- groupForKey(String) - Method in class MaskIntersectionAssigner
-
- GroupingRoot - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a set of definitions of classes can be collectively grouped using this class.
- GroupMapByName<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped
-
Adds items to aggregate structures identified uniquely by a name, and allows these items to be
later outputted.
- GroupMapByName(String, String, Supplier<T>) - Constructor for class GroupMapByName
-
Creates a group-map.
- groupNameSet() - Method in class IndexedCSVRows
-
- groupsForImage(SplitString) - Method in class ComparisonSharedState
-
- growBuffer(Point3i, Point3i, Optional<Extent>, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels
-
Grows the voxel buffer in the positive and negative directions by a certain amount.
- growBuffer(Point3i, Point3i, Optional<Extent>) - Method in class ObjectMask
-
Grows the object-mask's voxel buffers in the positive and negative directions by a certain
amount.
- growBy(Tuple3i, Extent) - Method in class BoundingBox
-
Grow the bounding-box by toAdd amount in each dimension in both positive and negative
directions.
- growBy(int) - Method in class Extent
-
Creates a new
Extent with
toAdd size
added to each dimension.
- growBy(ReadableTuple3i) - Method in class Extent
-
Creates a new
Extent with
toAdd size
added to each respective
dimension.
- growToZ(int, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels
-
Grows a single z-sliced
BoundedVoxels by duplicating the slice across the z-dimension
sizeZ number of times.
- growToZ(int) - Method in class ObjectMask
-
Grows a single z-sliced
ObjectMask by duplicating the slice across the z-dimension
sizeZ number of times.
- guaranteedImageAttributes() - Method in class AssignmentGenerator
-
- guaranteedImageAttributes() - Method in class ChannelGenerator
-
- guaranteedImageAttributes() - Method in class ObjectsAsGrayscaleGenerator
-
- guaranteedImageAttributes() - Method in class ObjectAsMaskGenerator
-
- guaranteedImageAttributes() - Method in class ObjectsAsRGBGenerator
-
- guaranteedImageAttributes() - Method in class DrawObjectOnStackGenerator
-
- guaranteedImageAttributes() - Method in class ExtractBoundingBoxAreaFromStackGenerator
-
- guaranteedImageAttributes() - Method in class DisplayStackGenerator
-
- guaranteedImageAttributes() - Method in class FlattenStackGenerator
-
- guaranteedImageAttributes() - Method in class RasterGenerator
-
Guarantees on the attributes of all images created by the generator.
- guaranteedImageAttributes() - Method in class RasterGeneratorDelegateToDisplayStack
-
- guaranteedImageAttributes() - Method in class RasterGeneratorDelegateToRaster
-
- guaranteedImageAttributes() - Method in class StackGenerator
-
- guaranteedImageAttributes() - Method in class MarksAsUniqueValueGenerator
-
- guaranteedImageAttributes() - Method in class MarksGeneratorBase
-
- GuessDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider
-
Guesses dimensions from an input-image if it exists.
- GuessDimensions() - Constructor for class GuessDimensions
-
- idAndIncrement() - Method in class MarkWithIdentifierFactory
-
- Identifiable - Interface in org.anchoranalysis.overlay.identifier
-
- IdentifiablePair<T extends Identifiable> - Class in org.anchoranalysis.mpp.pair
-
Pair of marks
- IdentifiablePair(T, T) - Constructor for class IdentifiablePair
-
- identifier(Optional<String>) - Method in class ExperimentIdentifier
-
Creates an identifier for the experiment
- identifier(Optional<String>) - Method in class ExperimentIdentifierAuto
-
- identifier(Optional<String>) - Method in class ExperimentIdentifierConstant
-
- identifier() - Method in class SingleFileInputBase
-
- identifier() - Method in interface InputFromManager
-
A unique name associated with the input.
- identifier() - Method in class InputFromManagerDelegate
-
- identifier() - Method in class MultiInput
-
- identifier() - Method in class Mark
-
- identifier() - Method in class CoupledManifests
-
- identifier() - Method in class ManifestCouplingDefinition
-
- identifierAsPath() - Method in interface InputFromManager
-
- IdentifierFromMark - Class in org.anchoranalysis.mpp.mark
-
- IdentifierFromMark() - Constructor for class IdentifierFromMark
-
- IdentifierFromOverlay - Class in org.anchoranalysis.overlay.identifier
-
- IdentifierFromOverlay() - Constructor for class IdentifierFromOverlay
-
- IdentifierGetter<T> - Interface in org.anchoranalysis.core.identifier.getter
-
Gets a unique identifier for a particular element at a particular iteration point.
- IdentifyDelegateToOverlays - Class in org.anchoranalysis.overlay.identifier
-
- IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection) - Constructor for class IdentifyDelegateToOverlays
-
- IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection, boolean) - Constructor for class IdentifyDelegateToOverlays
-
- IdentifyFromIteration<T> - Class in org.anchoranalysis.core.identifier.getter
-
Identify an element uniquely only by its iteration timepoint.
- IdentifyFromIteration() - Constructor for class IdentifyFromIteration
-
- IdentifyObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
-
Assigns a unique id number to each object.
- IdentifyObjects() - Constructor for class IdentifyObjects
-
- Identity - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- Identity() - Constructor for class Identity
-
- IdentityImposeValueRelationToHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- IdentityImposeValueRelationToHistogram() - Constructor for class IdentityImposeValueRelationToHistogram
-
- idFor(ObjectWithProperties, int) - Method in class ObjectDrawAttributes
-
ID for a particular object
- IfCondition<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.conditional
-
The result of featureCondition is compared to a threshold, and then either the underlying feature
is calculated (positive case), or featureElse is (negative case)
- IfCondition() - Constructor for class IfCondition
-
- IfConditionWithinRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
Calculates a value if a condition lies within a certain range, otherwise returns constants
- IfConditionWithinRange() - Constructor for class IfConditionWithinRange
-
- IfElse - Class in org.anchoranalysis.image.io.bean.object.draw
-
Branches to two different writers depending on a binary condition.
- IfElse(IfElse.Condition, DrawObject, DrawObject) - Constructor for class IfElse
-
- IfElse() - Constructor for class IfElse
-
- IfElse.Condition - Interface in org.anchoranalysis.image.io.bean.object.draw
-
- IfGreaterThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Calculates a level from the first delegate and if greater than a threshold, recalculates from a
second delegate.
- IfGreaterThan() - Constructor for class IfGreaterThan
-
- IfHighLow - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation iff first==HIGH and second==LOW then LOW voxelwise on both
masks, modifying {mask} with the result.
- IfHighLow() - Constructor for class IfHighLow
-
- IfIncrementingNumberRequested - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer
-
Multiplexes between two
PathPrefixers depending on whether an
incrementing number
sequence was output was requested.
- IfIncrementingNumberRequested() - Constructor for class IfIncrementingNumberRequested
-
- IfKeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask is returned if a condition on key-values is satisfied otherwise maskElse is returned.
- IfKeyValueCondition() - Constructor for class IfKeyValueCondition
-
- IfLessThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Calculates a level from the first delegate and if less than a threshold, recalculates from a
second delegate.
- IfLessThan() - Constructor for class IfLessThan
-
- IfNotEmpty - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask is returned if it's non-empty (at least one on voxel) otherwise
maskElse is returned.
- IfNotEmpty() - Constructor for class IfNotEmpty
-
- IfObjectFilter - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask is returned if the mask (treated as an object) passed an object-filter,
otherwise maskElse is returned.
- IfObjectFilter() - Constructor for class IfObjectFilter
-
- ifOptionWithoutArgument(String, Consumer<T>) - Method in class AddOptionsFromCommandLine
-
Executes consumer if an option exists without any argument.
- ifOptionWithSingleArgument(String, CheckedBiConsumer<T, String, E>) - Method in class AddOptionsFromCommandLine
-
Executes consumer if an option exists with a single argument.
- IfOutsideRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
Clamps a value if it lies outside the range - instead returning particular constants if below or
above an acceptable range
- IfOutsideRange() - Constructor for class IfOutsideRange
-
- IfParamEqual - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Multiplexes between two object-collection-providers depending on whether a parameter value equals
a particular string
- IfParamEqual() - Constructor for class IfParamEqual
-
- IfParamEquals - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
- IfParamEquals() - Constructor for class IfParamEquals
-
- IfPredicateBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
Base class which multiplexes between the current mask and an alternative depending if a condition
is met.
- IfPredicateBase() - Constructor for class IfPredicateBase
-
- ifPresent(Optional<S>, CheckedConsumer<S, E>) - Static method in class OptionalUtilities
-
- ifPresentSingle(String, CheckedConsumer<String, E>) - Method in class CommandLineExtracter
-
Executes a
Consumer if an option is present.
- ifPresentSingle(String, CheckedConsumer<String, E>) - Method in class AddOptionsFromCommandLine
-
- IfRelativeToDirectory - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
Multiplexes between two namers depending on if the relative-to-directory option is
selected.
- IfRelativeToDirectory() - Constructor for class IfRelativeToDirectory
-
- IfStackExists - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current mask is a particular stack exists (at least one on voxel) otherwise
maskElse is returned.
- IfStackExists() - Constructor for class IfStackExists
-
- IfVoxelZero - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Creates a new channel which is a merged version of two input channels according to rules.
- IfVoxelZero() - Constructor for class IfVoxelZero
-
- IgnoreUnderscorePrefix - Class in org.anchoranalysis.io.output.bean.enabled
-
All outputs are allowed unless the name's first character is an underscore.
- IgnoreUnderscorePrefix() - Constructor for class IgnoreUnderscorePrefix
-
- IgnoreUnderscorePrefixUnless - Class in org.anchoranalysis.io.output.bean.rules
-
Like
IgnoreUnderscorePrefix for all first and level-outputs unless a particular outputs
are explicitly specified.
- IgnoreUnderscorePrefixUnless(StringSet) - Constructor for class IgnoreUnderscorePrefixUnless
-
Create with first-level output names
- IgnoreUnderscorePrefixUnless() - Constructor for class IgnoreUnderscorePrefixUnless
-
- image() - Method in class MarksInitialization
-
- ImageAssignLabel<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Assigns a label to each image and copies into subdirectories for each label, and creates a
labelling CSV.
- ImageAssignLabel() - Constructor for class ImageAssignLabel
-
- ImageBean<T> - Class in org.anchoranalysis.image.bean
-
- ImageBean() - Constructor for class ImageBean
-
- ImageCounter<T> - Interface in org.anchoranalysis.plugin.annotation.counter
-
Counts images on aggregate, some with associated annotations, others without.
- ImageCounterList<T extends Assignment<ObjectMask>> - Class in org.anchoranalysis.plugin.annotation.counter
-
Allows operations to be applied to several
ImageCounters collectively.
- ImageCounterList() - Constructor for class ImageCounterList
-
- ImageCounterWithStatistics<T> - Interface in org.anchoranalysis.plugin.annotation.counter
-
- ImageCSVLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
- ImageCSVLabeller() - Constructor for class ImageCSVLabeller
-
- ImageCSVLabellerInitialization - Class in org.anchoranalysis.plugin.image.task.labeller
-
- ImageCSVLabellerInitialization(FileLabelMap<String>) - Constructor for class ImageCSVLabellerInitialization
-
- ImageFileAttributes - Class in org.anchoranalysis.image.core.stack
-
Timestamps and other metadata associated with an image file-path, but not with the file's
contents.
- ImageFileAttributes(Path, ZonedDateTime, ZonedDateTime) - Constructor for class ImageFileAttributes
-
- ImageFileEncoding - Class in org.anchoranalysis.io.bioformats.copyconvert
-
How values are encoded into an image-file.
- ImageFileEncoding(boolean, boolean, int) - Constructor for class ImageFileEncoding
-
- ImageFileFormat - Enum in org.anchoranalysis.core.format
-
A type of image format that are read/written to the filesystem, together with the extensions it
may use.
- ImageFileShape - Class in org.anchoranalysis.io.bioformats.copyconvert
-
How to shape the image (across various dimensions) after the copying
- ImageFileShape(Dimensions, int, int) - Constructor for class ImageFileShape
-
- ImageInitialization - Class in org.anchoranalysis.image.bean.nonbean.init
-
- ImageInitialization(SharedObjects) - Constructor for class ImageInitialization
-
- ImageInitialization(SharedObjects, Optional<ImageSizeSuggestion>) - Constructor for class ImageInitialization
-
- ImageInitializationFactory - Class in org.anchoranalysis.image.io
-
- ImageIOException - Exception in org.anchoranalysis.image.io
-
- ImageIOException(String) - Constructor for exception ImageIOException
-
- ImageIOException(String, Throwable) - Constructor for exception ImageIOException
-
- ImageIOWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer
-
- ImageIOWriter() - Constructor for class ImageIOWriter
-
- ImageJConversionException - Exception in org.anchoranalysis.io.imagej.convert
-
When conversion to ImageJ data/type is not possible, or an error occurs during conversion.
- ImageJConversionException(String) - Constructor for exception ImageJConversionException
-
Creates with a message.
- ImageJConversionException(Exception) - Constructor for exception ImageJConversionException
-
Creates with a message.
- ImageJRasterWriter - Class in org.anchoranalysis.io.imagej.bean.stack.writer
-
Base class for writing a raster using ImageJ.
- ImageJRasterWriter() - Constructor for class ImageJRasterWriter
-
- ImageLabelAnnotation - Class in org.anchoranalysis.annotation.image
-
A single label that is associated with an image.
- ImageLabelAnnotation(String) - Constructor for class ImageLabelAnnotation
-
- ImageLabelAnnotationReader - Class in org.anchoranalysis.annotation.io.image
-
- ImageLabelAnnotationReader() - Constructor for class ImageLabelAnnotationReader
-
- ImageLabelAnnotationWriter - Class in org.anchoranalysis.annotation.io.image
-
- ImageLabelAnnotationWriter() - Constructor for class ImageLabelAnnotationWriter
-
- ImageLabeller<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Associates a label with an image.
- ImageLabeller() - Constructor for class ImageLabeller
-
- ImageLabellerStringMap<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Maps one set of labels to another
- ImageLabellerStringMap() - Constructor for class ImageLabellerStringMap
-
- ImageLabellerStringMapInitialization<T> - Class in org.anchoranalysis.plugin.image.task.labeller
-
- ImageLabellerStringMapInitialization(Map<String, String>, T) - Constructor for class ImageLabellerStringMapInitialization
-
- ImageLabelStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
-
Assigns a single label per image, as a whole.
- ImageLabelStrategy() - Constructor for class ImageLabelStrategy
-
- ImageMetadata - Class in org.anchoranalysis.image.core.stack
-
Information about an image, but not about the intensity or content of image voxels.
- ImageMetadata(Dimensions, int, int, boolean, int, ImageFileAttributes, Optional<ZonedDateTime>) - Constructor for class ImageMetadata
-
- ImageMetadataInput - Class in org.anchoranalysis.image.io.stack.input
-
An input that provides a
ImageMetadata but only lazily when first called.
- ImageMetadataInput(NamedFile, CheckedSupplier<ImageMetadata, ImageIOException>) - Constructor for class ImageMetadataInput
-
Create for a particular file and metadata.
- ImageMetadataReader - Class in org.anchoranalysis.image.io.bean.stack.metadata.reader
-
- ImageMetadataReader() - Constructor for class ImageMetadataReader
-
- ImageMoments - Class in org.anchoranalysis.math.statistics.moment
-
The first moment (mean) and eigenvalues of the second moments (covariance) from a matrix of
points.
- ImageMoments(DoubleMatrix2D, boolean, boolean) - Constructor for class ImageMoments
-
Calculates the second-moments from the covariance of a matrix of points.
- ImageMomentsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
A base class for features that are calculated using image-moments.
- ImageMomentsBase() - Constructor for class ImageMomentsBase
-
- ImageSize - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
Summarizes the size of images.
- ImageSize() - Constructor for class ImageSize
-
- ImageSizeSuggestion - Interface in org.anchoranalysis.image.core.dimensions.size.suggestion
-
A suggestion on a size for an image.
- ImageSizeSuggestionFactory - Class in org.anchoranalysis.image.core.dimensions.size.suggestion
-
- ImageTimestampsAttributes - Class in org.anchoranalysis.image.io.stack.input
-
- ImageTimestampsAttributes(ImageFileAttributes, Optional<ZonedDateTime>) - Constructor for class ImageTimestampsAttributes
-
- ImageTimestampsAttributesFactory - Class in org.anchoranalysis.io.bioformats.metadata
-
- ImgLib2Lanczos - Class in org.anchoranalysis.image.bean.interpolator
-
- ImgLib2Lanczos() - Constructor for class ImgLib2Lanczos
-
- ImgLib2Linear - Class in org.anchoranalysis.image.bean.interpolator
-
- ImgLib2Linear() - Constructor for class ImgLib2Linear
-
- immutableAdd(Point2i, Point2i) - Static method in class Point2i
-
Adds two points immutably.
- immutableAdd(Tuple3d, Tuple3d) - Static method in class Point3d
-
Adds two tuples immutably.
- immutableAdd(Point3d, int, int, int) - Static method in class Point3d
-
Adds values to a point immutably.
- immutableAdd(ReadableTuple3i, ReadableTuple3i) - Static method in class Point3i
-
Adds two tuples immutably.
- immutableAdd(ReadableTuple3i, int, int, int) - Static method in class Point3i
-
Adds values to a tuple immutably.
- immutableScale(Tuple3d, int) - Static method in class Point3d
-
Scales a tuple immutably.
- immutableScale(ReadableTuple3i, int) - Static method in class Point3i
-
Multiplies each component by factor without changing any values in an existing point.
- immutableSubtract(Tuple3d, Tuple3d) - Static method in class Point3d
-
- immutableSubtract(Tuple3i, Tuple3d) - Static method in class Point3d
-
- immutableSubtract(ReadableTuple3i, ReadableTuple3i) - Static method in class Point3i
-
Subtracts two tuples immutably.
- ImposeMinima - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Imposes minima in seed locations on the input-channel before performing the segmentation
- ImposeMinima() - Constructor for class ImposeMinima
-
- imposeMinima(Channel, ObjectCollection, Optional<ObjectMask>) - Method in class MinimaImposition
-
- imposeMinima(Channel, ObjectCollection, Optional<ObjectMask>) - Method in class MinimaImpositionGrayscaleReconstruction
-
- imposeMinimumRadius(double) - Method in class FitResult
-
- ImposeResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
Adds an explicit
Resolution to an image after it has been read.
- ImposeResolution() - Constructor for class ImposeResolution
-
- IncludeBeanFactory - Class in org.anchoranalysis.bean.xml.factory
-
Defines an
AnchorBean in a separate file on the file-system.
- IncludeBeanFactory() - Constructor for class IncludeBeanFactory
-
- includeFirst() - Method in class MergedPairsInclude
-
- includeFirstOrSecond() - Method in class MergedPairsInclude
-
- includeGroupInExperiment(boolean) - Method in class FeatureSource
-
Iff true, group columns are added to the CSV exports, and other group exports may occur in
sub-directories.
- includeGroupInExperiment(boolean) - Method in class FromHistogram
-
- includeGroupInExperiment(boolean) - Method in class FromImage
-
- includeGroupInExperiment(boolean) - Method in class FromImageMetadata
-
- includeGroupInExperiment(boolean) - Method in class FromObjects
-
If either a group-generator is defined or there's more than one provider, then groups should
be included.
- IncludeListBeanFactory<T> - Class in org.anchoranalysis.bean.xml.factory
-
Like
ListBeanFactory but also includes elements in other lists defined in the
include tag.
- IncludeListBeanFactory() - Constructor for class IncludeListBeanFactory
-
Default constructor.
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaOr
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaPair
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class ArbitraryPointCommon
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class BoundingBoxIntersection
-
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class AddCriteriaFeatureRelationThreshold
-
- IncludeMarksFailureException - Exception in org.anchoranalysis.mpp.feature.addcriteria
-
- IncludeMarksFailureException(String) - Constructor for exception IncludeMarksFailureException
-
- IncludeMarksFailureException(Exception) - Constructor for exception IncludeMarksFailureException
-
- includeMerged() - Method in class MergedPairsInclude
-
- IncludeRandomObjects - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points
-
1.
- IncludeRandomObjects() - Constructor for class IncludeRandomObjects
-
- includeSecond() - Method in class MergedPairsInclude
-
- IncompleteElementRange - Interface in org.anchoranalysis.io.manifest.sequencetype
-
An incomplete range of discrete integers (like
IndexRangeSeek but with a
string-representation for each index.
- IncorrectImageSizeException - Exception in org.anchoranalysis.image.core.dimensions
-
When an image has incompatible image-size with expectations.
- IncorrectImageSizeException(String) - Constructor for exception IncorrectImageSizeException
-
Create with a message.
- IncorrectVoxelTypeException - Exception in org.anchoranalysis.image.voxel.datatype
-
- IncorrectVoxelTypeException(String) - Constructor for exception IncorrectVoxelTypeException
-
Create with only a message.
- IncorrectVoxelTypeException(Throwable) - Constructor for exception IncorrectVoxelTypeException
-
Create with only a cause.
- incr(int) - Method in class AggIDCounter
-
- incr(Reporting<S>) - Method in class PeriodTriggerBank
-
- IncreaseFeatureCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
-
- IncreaseFeatureCondition(FeatureEvaluator<FeatureInputSingleObject>) - Constructor for class IncreaseFeatureCondition
-
- increasingIntegers(OutputPatternIntegerSuffix) - Method in class OutputSequenceFactory
-
- IncreasingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype
-
Indices must be integers that always increase as added.
- IncreasingIntegers() - Constructor for class IncreasingIntegers
-
- increment() - Method in class Counter
-
Increases the counter by one.
- increment(double) - Method in class RunningSum
-
Adds a new item to the sum, and increments the count by 1.
- increment(double, long) - Method in class RunningSum
-
Increments both the sum and count by particular values.
- increment(RunningSum) - Method in class RunningSum
-
Increments (adds) an existing
RunningSum to the current.
- increment(Point2i) - Method in class RunningSumPoint
-
Increments the running-sum by a
Point2i.
- increment(Point2d) - Method in class RunningSumPoint
-
Increments the running-sum by a
Point2d.
- increment(Point3i) - Method in class RunningSumPoint
-
Increments the running-sum by a
Point3i.
- increment(Point3d) - Method in class RunningSumPoint
-
Increments the running-sum by a
Point3d.
- increment(Tuple3d) - Method in class Tuple3d
-
Increments each component's value by the corresponding value in a
Tuple3d.
- incrementBy(int) - Method in class Counter
-
Increases the counter by a specific value.
- incrementChild() - Method in class ProgressMultiple
-
Increments the current child tracker to the next child.
- incrementCount(T) - Method in class SummarizerImageMetadata
-
- incrementCount(T) - Method in class FrequencyMap
-
- incrementCounter() - Method in class RecordingCounter
-
Increments the counter.
- incrementEnergy(double) - Method in class Aggregator
-
- incrementIndexOnly() - Method in class KernelPointCursor
-
Increments the current index state by one, without changing the current point state.
- incrementingByOne(String, OutputterChecked) - Method in class OutputSequenceStackFactory
-
Creates an sequence of stacks in a subdirectory with a number in the outputted file name that
increments each time by one.
- incrementingByOne(OutputPatternIntegerSuffix) - Method in class OutputSequenceFactory
-
Writes elements to directory, with an incrementing integer in the filename.
- incrementingByOneCurrentDirectory(String, String, int, OutputterChecked) - Method in class OutputSequenceStackFactory
-
Creates a sequence of stacks in the current context's directory with a number in the
outputted file name that increments each time by one.
- incrementingByOneCurrentDirectory(String, String, int) - Method in class OutputSequenceFactory
-
Writes elements to the current directory, with an incrementing integer in the filename.
- incrementingByOneStream(OutputPatternIntegerSuffix, Stream<T>) - Method in class OutputSequenceFactory
-
Writes file for each element in a stream with an incrementing integer sequence in the
outputted file-name.
- incrementingIntegers(OutputPatternIntegerSuffix, int, int) - Method in class OutputSequenceFactory
-
- IncrementingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype
-
- IncrementingIntegers() - Constructor for class IncrementingIntegers
-
- IncrementingIntegers(int) - Constructor for class IncrementingIntegers
-
- IncrementingIntegers(int, int) - Constructor for class IncrementingIntegers
-
- IncrementingNumber - Class in org.anchoranalysis.io.output.bean.path.prefixer
-
Outputs an incrementing number for each output that occurs.
- IncrementingNumber(String) - Constructor for class IncrementingNumber
-
- IncrementingNumber() - Constructor for class IncrementingNumber
-
- incrementKernelAcceptance(int) - Method in class Aggregator
-
- incrementKernelProp(int) - Method in class Aggregator
-
- incrementSize(double) - Method in class Aggregator
-
- incrementTemperature(double) - Method in class Aggregator
-
- incrementValue(int) - Method in class Histogram
-
Increments the count for a particular value by one.
- incrementValueBy(int, int) - Method in class Histogram
-
Increments the count for a particular value.
- incrementValueBy(int, long) - Method in class Histogram
-
- incrementX() - Method in class KernelPointCursor
-
Increments the point and associated index by one in the X dimension.
- incrementX() - Method in class Point2i
-
Increments the X component's value by one.
- incrementX(int) - Method in class Point2i
-
Increments the X component's value by a shift.
- incrementX(double) - Method in class Tuple3d
-
Increments the X component's value by a shift.
- incrementX() - Method in class Tuple3i
-
Increments the X component's value by one.
- incrementX(int) - Method in class Tuple3i
-
Increments the X component's value by a shift.
- incrementXTwice() - Method in class KernelPointCursor
-
Increments the point and associated index by two in the X dimension.
- incrementY() - Method in class KernelPointCursor
-
Increments the point and associated index by one in the Y dimension.
- incrementY() - Method in class Point2i
-
Increments the Y component's value by one.
- incrementY(int) - Method in class Point2i
-
Increments the Y component's value by a shift.
- incrementY(double) - Method in class Tuple3d
-
Increments the Y component's value by a shift.
- incrementY() - Method in class Tuple3i
-
Increments the Y component's value by one.
- incrementY(int) - Method in class Tuple3i
-
Increments the Y component's value by a shift.
- incrementYTwice() - Method in class KernelPointCursor
-
Increments the point and associated index by two in the Y dimension.
- incrementZ() - Method in class KernelPointCursor
-
Increments the point by one in the Z dimension.
- incrementZ(double) - Method in class Tuple3d
-
Increments the Z component's value by a shift.
- incrementZ() - Method in class Tuple3i
-
Increments the Z component's value by one.
- incrementZ(int) - Method in class Tuple3i
-
Increments the Z component's value by a shift.
- incrementZTwice() - Method in class KernelPointCursor
-
Increments the point by two in the Z dimension.
- IndependentChannels - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Converts each channel independently and creates a single-channeled stack from the conversion.
- IndependentChannels() - Constructor for class IndependentChannels
-
- index(int, int, Extent) - Method in enum OrientationChange
-
Determines the index in a output-array to put an element after applying the
orientation-change.
- index(int, int, int, Extent) - Method in enum OrientationChange
-
Like {#link determineOutputIndex(int,int,Extent)} but also accepts an index.
- index(int) - Method in class IntegerRange
-
Maps an original integer to it's index from (0..size]
- Indexable - Class in org.anchoranalysis.core.index
-
Holds a single-index which is hashable and comparable.
- Indexable(int) - Constructor for class Indexable
-
- IndexableMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy
-
- IndexableMarksWithEnergy(int, MarksWithEnergyBreakdown) - Constructor for class IndexableMarksWithEnergy
-
- IndexableOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
An output-name with an index somehow appended or prepended in a particular style.
- IndexableOutputNameStyle() - Constructor for class IndexableOutputNameStyle
-
- IndexableOutputNameStyle(String) - Constructor for class IndexableOutputNameStyle
-
- IndexableOutputNameStyle(IndexableOutputNameStyle) - Constructor for class IndexableOutputNameStyle
-
Copy constructor
- IndexableOverlays - Class in org.anchoranalysis.overlay
-
- IndexableOverlays(int, OverlayCollection) - Constructor for class IndexableOverlays
-
- IndexByChannel<T> - Class in org.anchoranalysis.mpp.index
-
- IndexByChannel() - Constructor for class IndexByChannel
-
- IndexByRegion<T> - Class in org.anchoranalysis.mpp.index
-
- IndexByRegion(VoxelPartitionFactory<T>, int, int) - Constructor for class IndexByRegion
-
- indexDistanceMaxToClosestPoint(Point3i, List<ContiguousVoxelPath>, int) - Static method in class FindMinimumDistance
-
The index of whichever of the ContiguousPixelPaths has the nearest point
- IndexedCSVRows - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
Stores the rows from the CSV file.
- IndexedCSVRows(ReadByLine, ColumnDefinition) - Constructor for class IndexedCSVRows
-
Creates an index of the rows of the CSV file according to a particular columnDefinition
- IndexedRegionBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- IndexedRegionBase() - Constructor for class IndexedRegionBase
-
- indexIncr(String) - Method in class SequenceMemory
-
- indexInitialPoint() - Method in class ContiguousVoxelPath
-
- indexOf(String) - Method in class FeatureNameMapToIndex
-
The index for a particular featureName
- indexOf(Mark) - Method in class VoxelizedMarksWithEnergy
-
- indexOf(Object) - Method in class UpdatableMarksList
-
- indexOf(Mark) - Method in class MarkCollection
-
- IndexRange - Interface in org.anchoranalysis.core.index.range
-
A range of discrete integers with a minimum and a maximum.
- IndexRangeNegative - Class in org.anchoranalysis.core.index.range
-
Specifying a sub-range of indices, tolerating also negative indices.
- IndexRangeNegative(int, int) - Constructor for class IndexRangeNegative
-
- IndexRangeNegativeFactory - Class in org.anchoranalysis.core.index.range
-
- IndexRangeSeek - Interface in org.anchoranalysis.core.index.range
-
A range of discrete integers, where one can always find the succeeding or preceding index.
- indexUniquePixel - Variable in class ColumnDefinition
-
- InferFromHeader - Class in org.anchoranalysis.plugin.io.bean.metadata.reader
-
Tries to construct the
ImageMetadata from EXIF and other metadata, if available, or
otherwise falls back to another reader.
- InferFromHeader() - Constructor for class InferFromHeader
-
- InferFromHeader(ImageMetadataReader, List<HeaderFormat>) - Constructor for class InferFromHeader
-
- informLatestState(T) - Method in class Kernel
-
Called every time a proposal is accepted, so a kernel can potentially keep track of the state
of the current image
- informLatestState(T) - Method in class KernelIndependent
-
- initBeforeCalc(KernelCalculationContext) - Method in class Kernel
-
- initBeforeCalc(KernelCalculationContext) - Method in class KernelIndependent
-
- initBeforeCalc(KernelCalculationContext) - Method in class KernelProposer
-
- initHeaders(String[]) - Method in class ColumnDefinition
-
- initHeaders(String[]) - Method in class Pairwise
-
- initHeaders(String[]) - Method in class Single
-
- InitializableBean<B,P extends BeanInitialization> - Class in org.anchoranalysis.bean.initializable
-
A bean that must be initialized with some parameters before being used.
- InitializableBean(BeanInitializer<P>, InitializationParameterAssigner) - Constructor for class InitializableBean
-
- InitializationContext - Class in org.anchoranalysis.experiment.io
-
Context for creating initialization-parameters.
- InitializationContext(InputOutputContext) - Constructor for class InitializationContext
-
- InitializationContext(InputOutputContext, Optional<ImageSizeSuggestion>) - Constructor for class InitializationContext
-
- InitializationFactory - Class in org.anchoranalysis.image.feature.calculator
-
- InitializationFactory - Class in org.anchoranalysis.plugin.image.task.stack
-
- InitializationParameterAssigner - Interface in org.anchoranalysis.bean.initializable.property
-
Assigns a parameter to a bean, if the bean accepts it.
- InitializationWithEnergyStack - Class in org.anchoranalysis.plugin.image.task.feature
-
- InitializationWithEnergyStack(EnergyStack, InitializationContext) - Constructor for class InitializationWithEnergyStack
-
- InitializationWithEnergyStack(ImageInitialization, EnergyStack) - Constructor for class InitializationWithEnergyStack
-
- initialize(P, Logger) - Method in class InitializableBean
-
Initializes the bean with the necessary parameters.
- initialize(FeatureInitialization, Logger) - Method in interface FeatureCalculationCache
-
Initializes the cache.
- initialize(ArrangeStack, List<RGBStack>) - Method in class RasterArranger
-
- initialize(List<Histogram>, Optional<Dictionary>) - Method in class VoxelScore
-
Initializes the voxels-score.
- initialize(ChannelGetter, InputOutputContext) - Method in class ChannelFilter
-
- initialize(Path) - Method in class Manifest
-
- initialize(BeanInstanceMap) - Method in class OutputWriteSettings
-
- initialize() - Method in class MarksWithEnergyBreakdown
-
- initialize(VoxelPartitionFactory<T>, int, int, int) - Method in class IndexByChannel
-
- initialize(MarksInitialization, Logger) - Method in class ReportFeatureEvaluator
-
- initialize(Generator<T>) - Method in class PeriodicSubdirectoryReporter
-
- initialize() - Method in class KernelProposer
-
- initialize() - Method in class TerminationCondition
-
- initialize() - Method in class TerminationConditionListOr
-
- initialize() - Method in class TriggerTerminationCondition
-
- initialize(List<Histogram>, Optional<Dictionary>) - Method in class CalculateLevelBase
-
- initialize(List<Histogram>, Optional<Dictionary>) - Method in class FromDictionaryBase
-
- initialize(List<Histogram>, Optional<Dictionary>) - Method in class IdentityImposeValueRelationToHistogram
-
- initialize(List<Histogram>, Optional<Dictionary>) - Method in class NormalizeByMax
-
- initialize(Logger) - Method in interface AfterCondition
-
- initialize(Logger) - Method in class IncreaseFeatureCondition
-
- initialize(Path) - Method in class BinaryOutcomeImageLabeller
-
- initialize(Path) - Method in class ImageCSVLabeller
-
- initialize(Path) - Method in class ImageLabeller
-
Should be called once before calling any other methods
- initialize(Path) - Method in class ImageLabellerStringMap
-
- initialize(KernelBirth<T>, KernelDeath<T>) - Method in class KernelReplace
-
Must be called before makeProposal
- initialize() - Method in class NumberIterations
-
- initialize() - Method in class UnchangedBase
-
- initialize() - Method in class UnchangedScore
-
- initialize() - Method in class UnchangedSize
-
- InitializeException - Exception in org.anchoranalysis.core.exception
-
An exception that occurs when initializing something, and it doesn't succeed
- InitializeException(String) - Constructor for exception InitializeException
-
Creates with a message, but without a cause.
- InitializeException(Throwable) - Constructor for exception InitializeException
-
Creates with a cause, but without a message.
- InitializeException(String, Throwable) - Constructor for exception InitializeException
-
Creates with message and cause.
- initializePhase(int) - Method in class HungarianAlgorithm
-
Initialize the next phase of the algorithm by clearing the committed workers and jobs sets
and by initializing the slack arrays to the values corresponding to the specified root
worker.
- initializeRecursive(P, Logger) - Method in class InitializableBean
-
Initializes this object, and all children objects, so long as they have P once a Bean
doesn't have P, the children are not evaluated.
- initializeRecursive(Logger) - Method in class NullParametersBean
-
Initialize this bean and any suitable child beans.
- initializeRecursive(FeatureInitialization, Logger) - Method in class FeatureList
-
Initializes all features in the list, and recursively any features they contain.
- initializeRecursive(FeatureInitialization, Logger) - Method in class SharedFeaturesSubset
-
Initialize all features in this instance, recursively also initializating any child-features.
- initializerForMarksBeans() - Static method in class MarksBean
-
Creates a property-initializes for MPP-Beans
- initialKernel() - Method in class KernelProposer
-
- initRecursiveWithInitializer(BeanInitializer<?>, Logger) - Method in class InitializableBean
-
Initializes the bean and recursively all contained beans (who have compatible initialization
requirements)
- initSource(int, int) - Method in interface ProcessChangedPointAbsoluteMasked
-
The value and offset for the source point (around which we process neighbors).
- initSource(Point3i, int, int) - Method in interface ProcessVoxelNeighbor
-
Specify the source-point (of which all the processed points are neighbors).
- initSource(int, int) - Method in interface ProcessVoxelNeighborAbsolute
-
The value and offset for the source point (around which we process neighbors).
- initSource(int, int) - Method in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class RandomCollectionWithAddCriteria
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class EnergySavedPairs
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in class UpdatableMarksList
-
- initUpdatableMarks(MemoForIndex, EnergyStack, Logger, SharedFeatures) - Method in interface UpdatableMarks
-
- initWithProposerSharedObjects(MarksInitialization, Logger) - Method in class KernelProposer
-
- input() - Method in class ExecutionArguments
-
Arguments to help determine the input to the experiment.
- INPUT_IMAGE - Static variable in class StackIdentifiers
-
The image used as the primary input for a task.
- InputArguments - Class in org.anchoranalysis.experiment.arguments
-
Arguments that can further specify an experiment's input in addition to its bean
specification.
- InputArguments() - Constructor for class InputArguments
-
- InputBound<T,S> - Class in org.anchoranalysis.experiment.task
-
Input for executing a task, associated with shared-state and other parameters.
- InputBound(T, S, Manifest, boolean, InputOutputContextStateful, InputOutputContextStateful) - Constructor for class InputBound
-
- InputContextParameters - Class in org.anchoranalysis.io.input
-
Additional parameters that offer context for many beans that provide input-functions.
- InputContextParameters() - Constructor for class InputContextParameters
-
- InputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path
-
SelectParam<Path> factory for inputs.
- InputFromManager - Interface in org.anchoranalysis.io.input
-
One particular input for processing.
- InputFromManagerDelegate<T extends InputFromManager> - Class in org.anchoranalysis.io.input
-
A base class for
InputFromManager-implementing classes that delegate to another.
- InputFromManagerDelegate(T) - Constructor for class InputFromManagerDelegate
-
- InputManager<T extends InputFromManager> - Class in org.anchoranalysis.io.input.bean
-
Base class for describing the inputs.
- InputManager() - Constructor for class InputManager
-
- InputManagerParameters - Class in org.anchoranalysis.io.input.bean
-
Parameters passed to an
InputManager to generate input-objects
- InputManagerParameters(Logger) - Constructor for class InputManagerParameters
-
Create with only a logger, and using sensible default values for the other fields.
- InputManagerParameters(InputContextParameters, Progress, ExecutionTimeRecorder, Logger) - Constructor for class InputManagerParameters
-
- InputManagerUnary<T extends InputFromManager> - Class in org.anchoranalysis.io.input.bean
-
- InputManagerUnary() - Constructor for class InputManagerUnary
-
- InputManagerWithStackReader<T extends InputFromManager> - Class in org.anchoranalysis.image.io.bean.stack.reader
-
- InputManagerWithStackReader() - Constructor for class InputManagerWithStackReader
-
- inputName() - Method in class StackWithMap
-
- inputName() - Method in class SegmentObjectsFromONNXModel
-
- inputName() - Method in class SegmentObjectsFromTensorFlowModel
-
- inputOutput(ExecutionArguments, OutputterChecked) - Method in class ExperimentFeedbackContext
-
- InputOutputContext - Interface in org.anchoranalysis.io.output.outputter
-
A context for performing input generally and outputting to a particular output-directory.
- InputOutputContextStateful - Class in org.anchoranalysis.experiment.task
-
- InputOutputContextStateful(ExecutionArguments, Outputter, ExecutionTimeRecorder, StatefulMessageLogger, ErrorReporter) - Constructor for class InputOutputContextStateful
-
- InputOutputContextSubdirectoryCache - Class in org.anchoranalysis.io.output.outputter
-
- InputOutputContextSubdirectoryCache(InputOutputContext, ManifestDirectoryDescription, boolean) - Constructor for class InputOutputContextSubdirectoryCache
-
- InputOutputExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.io
-
- InputOutputExperiment() - Constructor for class InputOutputExperiment
-
- InputReadFailedException - Exception in org.anchoranalysis.io.input
-
- InputReadFailedException(String) - Constructor for exception InputReadFailedException
-
- InputReadFailedException(Throwable) - Constructor for exception InputReadFailedException
-
- InputReadFailedException(String, Throwable) - Constructor for exception InputReadFailedException
-
- inputs(InputManagerParameters) - Method in class AnnotationInputManager
-
- inputs(InputManagerParameters) - Method in class InputManager
-
Creates a list of inputs given particular parameters.
- inputs(InputManagerParameters) - Method in class InputManagerUnary
-
- inputs() - Method in class InputsWithDirectory
-
The inputs.
- inputs(InputManagerParameters) - Method in class MultiInputManager
-
- inputs(InputManagerParameters) - Method in class AnnotationComparisonInputManager
-
- inputs(InputManagerParameters) - Method in class GroupFiles
-
- inputs(InputManagerParameters) - Method in class NamedChannels
-
- inputs(InputManagerParameters) - Method in class NamedChannelsAppend
-
- inputs(InputManagerParameters) - Method in class Concatenate
-
- inputs(InputManagerParameters) - Method in class NamedFiles
-
- inputs(InputManagerParameters) - Method in class NamedFilesWithDirectory
-
- inputs(InputManagerParameters) - Method in class CoupledManifestsInputManager
-
- inputs(InputManagerParameters) - Method in class ConvertNamedChannelsToStack
-
- inputs(InputManagerParameters) - Method in class Stacks
-
- inputs(ImageInitialization, Logger) - Method in class ExportObjectsBase
-
- inputs(InputManagerParameters) - Method in class FromCSVInputManager
-
- inputs(InputManagerParameters) - Method in class MultiInputManagerQuick
-
- inputs(InputManagerParameters) - Method in class NamedChannelsQuick
-
- inputSelectParam(CommandLine) - Static method in class SelectParamFactory
-
Can point to either:
a path ending in .xml, assumed to BeanXML for an input manager
a directory, set as an the inputDirectory in the input-context
a string with a wild-card, assumed to be a glob, set into the input-context as a glob
a string with a period and without any forward or backwards slashes, set into the
input-context as an extension to match
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class InputManagerUnary
-
Calculates the inputs to return given the inputs from the delegate.
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class BranchIfDebug
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class Exclude
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class FilterCSVColumn
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class FilterDescriptiveName
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class FilterIfDebug
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class Limit
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class Shuffle
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class ShuffleIfRequested
-
- inputsFromDelegate(InputsWithDirectory<T>, InputManagerParameters) - Method in class SortAlphabetically
-
- InputsWithDirectory<T extends InputFromManager> - Class in org.anchoranalysis.io.input
-
All inputs for an experiment, together with any parent directory which is specified as a parent
for these inputs.
- InputsWithDirectory(List<T>) - Constructor for class InputsWithDirectory
-
Creates without any parent directory.
- InputsWithDirectory(List<T>, Optional<Path>) - Constructor for class InputsWithDirectory
-
- inputType() - Method in class Feature
-
The class corresponding to feature input-type.
- inputType() - Method in class FeatureBinary
-
- inputType() - Method in class FeatureFromList
-
- inputType() - Method in class FeatureGeneric
-
- inputType() - Method in class FeatureUnary
-
- inputType() - Method in class FeatureResults
-
- inputType() - Method in class FeatureEnergy
-
- inputType() - Method in class FeatureHistogram
-
- inputType() - Method in class FeatureImageMetadata
-
- inputType() - Method in class FeatureStack
-
- inputType() - Method in class FeatureObjectCollection
-
- inputType() - Method in class FeaturePairObjects
-
- inputType() - Method in class FeatureSingleObject
-
- inputType() - Method in class AsSingle
-
- inputType() - Method in class FeatureAllMemo
-
- inputType() - Method in class FeaturePairMemo
-
- inputType() - Method in class FeatureSingleMemo
-
- inputType() - Method in class FeatureMarkCollection
-
- inputType() - Method in class FeatureMark
-
- inputType() - Method in class FromDimensionsBase
-
- inputType() - Method in class FeatureSingleObjectFromShared
-
- inputType() - Method in class AsMark
-
- inputType() - Method in class AsObject
-
- inputTypesExpected() - Method in class Task
-
Highest class(es) that will function as a valid input.
- InputTypesExpected - Class in org.anchoranalysis.experiment.task
-
A list of base (parent) classes for input-types that a task expects
- InputTypesExpected(Class<? extends InputFromManager>) - Constructor for class InputTypesExpected
-
- inputTypesExpected() - Method in class HelloWorld
-
- inputTypesExpected() - Method in class AggregateAnnotations
-
- inputTypesExpected() - Method in class CompareAnnotations
-
- inputTypesExpected() - Method in class ExportFeatures
-
- inputTypesExpected() - Method in class FeatureSource
-
Highest class(es) that will function as a valid input.
- inputTypesExpected() - Method in class FromHistogram
-
- inputTypesExpected() - Method in class FromImage
-
- inputTypesExpected() - Method in class FromImageMetadata
-
- inputTypesExpected() - Method in class GroupedStackBase
-
- inputTypesExpected() - Method in class ImageAssignLabel
-
- inputTypesExpected() - Method in class RasterTask
-
- inputTypesExpected() - Method in class ScaleImage
-
- inputTypesExpected() - Method in class SegmentInstanceWithModel
-
- inputTypesExpected() - Method in class ExtractSlice
-
- inputTypesExpected() - Method in class CombineCSV
-
- inputTypesExpected() - Method in class CopyFiles
-
- inputTypesExpected() - Method in class SummarizeInputs
-
- inputTypesExpected() - Method in class ConvertNamedChannels
-
- inputTypesExpected() - Method in class Develop
-
- inputTypesExpected() - Method in class ExportReportFeaturesFromManifest
-
- inputTypesExpected() - Method in class ExportReportFeaturesFromMulti
-
- inputTypesExpected() - Method in class FromObjects
-
- inputTypesExpected() - Method in class ExportObjectsAsCroppedImages
-
- inputTypesExpected() - Method in class ExportObjectsFromCSV
-
- inputTypesExpected() - Method in class SegmentMarksFromImage
-
- insertAfter(List<Point3i>) - Method in class ContiguousVoxelPath
-
Inserts points at end of existing path.
- insertBefore(List<Point3i>) - Method in class ContiguousVoxelPath
-
Inserts points before existing path.
- insertBeginning(String) - Method in class FeatureNameList
-
Inserts a new feature-name at the beginning of the list.
- insertBeginning(String[]) - Method in class FeatureNameList
-
Inserts new feature-names at the beginning of the list.
- InsertRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Generates an out string where $digit$ is replaced with the #digit group from a regex
- InsertRegExGroups() - Constructor for class InsertRegExGroups
-
- InsertRegExGroups(RegEx, String) - Constructor for class InsertRegExGroups
-
- instance() - Static method in class NullInitialization
-
- instance() - Static method in class ExecutionTimeRecorderIgnore
-
Singleton instance.
- INSTANCE - Static variable in class NoSharedState
-
- instance() - Static method in class FeatureInputNull
-
A singleton instance.
- instance() - Static method in class DefaultChildCacheFinder
-
- instance() - Static method in class ChannelFactory
-
- INSTANCE - Static variable in class FloatVoxelType
-
A singleton instance of the type.
- INSTANCE - Static variable in class SignedShortVoxelType
-
A singleton instance of the type.
- INSTANCE - Static variable in class UnsignedByteVoxelType
-
A singleton instance of the type.
- INSTANCE - Static variable in class UnsignedIntVoxelType
-
A singleton instance of the type.
- INSTANCE - Static variable in class UnsignedShortVoxelType
-
A singleton instance of the type.
- instance() - Static method in class VoxelsFactory
-
Singleton instance.
- instance() - Static method in class ConfigureBioformatsLogging
-
- INSTANCE - Static variable in class All
-
A singleton instance of
All.
- INSTANCE - Static variable in class IgnoreUnderscorePrefix
-
- INSTANCE - Static variable in class None
-
A singleton instance of
None.
- INSTANCE - Static variable in class Permissive
-
- instance() - Static method in class RegionMapSingleton
-
- instance() - Static method in class ErrorNodeNull
-
- instance() - Static method in class RootPathMap
-
- InsufficientPointsException - Exception in org.anchoranalysis.mpp.bean.points.fitter
-
- InsufficientPointsException() - Constructor for exception InsufficientPointsException
-
- InsufficientPointsException(String, Throwable) - Constructor for exception InsufficientPointsException
-
- InsufficientPointsException(String) - Constructor for exception InsufficientPointsException
-
- InsufficientPointsException(Throwable) - Constructor for exception InsufficientPointsException
-
- IntBinaryOperation - Interface in org.anchoranalysis.core.functional.unchecked
-
A binary operation on two int-values that produces an int.
- IntegerList - Class in org.anchoranalysis.bean.primitive
-
A bean defining a list of
Integers.
- IntegerList(Integer...) - Constructor for class IntegerList
-
Constructs with one or more values added to the list.
- IntegerListFactory - Class in org.anchoranalysis.bean.xml.factory.primitive
-
- IntegerListFactory() - Constructor for class IntegerListFactory
-
- IntegerRange - Class in org.anchoranalysis.plugin.io.multifile
-
- IntegerRange(int) - Constructor for class IntegerRange
-
- IntegerRange(int, int) - Constructor for class IntegerRange
-
- IntegerSet - Class in org.anchoranalysis.bean.primitive
-
- IntegerSet(Integer...) - Constructor for class IntegerSet
-
Constructs with one or more values added to the list.
- IntegerSet() - Constructor for class IntegerSet
-
- integerSet() - Method in class OverlayCollection
-
- IntegerSetFactory - Class in org.anchoranalysis.bean.xml.factory.primitive
-
- IntegerSetFactory() - Constructor for class IntegerSetFactory
-
- IntegerSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
Outputs a file-name involving an integer of length numberDigits with leading zeros.
- IntegerSuffixOutputNameStyle() - Constructor for class IntegerSuffixOutputNameStyle
-
- IntegerSuffixOutputNameStyle(String, int) - Constructor for class IntegerSuffixOutputNameStyle
-
- IntegerSuffixOutputNameStyle(String, String, int) - Constructor for class IntegerSuffixOutputNameStyle
-
- Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Calculates a statistic from the intensity values covered by a single object-mask in a channel.
- Intensity() - Constructor for class Intensity
-
- Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity
-
The intensity of a particular channel of the stack, by default the mean-intensity.
- Intensity() - Constructor for class Intensity
-
- Intensity - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- Intensity() - Constructor for class Intensity
-
- IntensityGradientBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
- IntensityGradientBase() - Constructor for class IntensityGradientBase
-
- IntensityGreaterEqualThan - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Only keep objects where at least one voxel (on a particular channel) has intensity greater or
equal to a threshold.
- IntensityGreaterEqualThan() - Constructor for class IntensityGreaterEqualThan
-
- intensityMax(Voxels<T>) - Static method in class IterateVoxelsAll
-
Finds the maximum intensity-value (as an int) among all voxels.
- IntensityMeanCalculator - Class in org.anchoranalysis.plugin.image.intensity
-
- IntensityMeanMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
- IntensityMeanMaxSlice() - Constructor for class IntensityMeanMaxSlice
-
- IntensityMeanShell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including
the original object-mask) and measures the mean intensity of this shell
- IntensityMeanShell() - Constructor for class IntensityMeanShell
-
- IntensityMeanShellBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a shell around an object-mask using a standard dilation and erosion process
- IntensityMeanShellBase() - Constructor for class IntensityMeanShellBase
-
- IntensityMeanShellMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including
the original object-mask) and measures the mean intensity of this shell
- IntensityMeanShellMaxSlice() - Constructor for class IntensityMeanShellMaxSlice
-
- IntensityMoments - Class in org.anchoranalysis.plugin.image.feature.bean.list
-
Calculate various moment-related statistics about the intensity of each channel of an image.
- IntensityMoments() - Constructor for class IntensityMoments
-
- interpolate(VoxelsUntyped, VoxelsUntyped) - Method in class Interpolator
-
Copies voxels slice-by-slice from source to destination performing necessary
interpolation.
- interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class Interpolator
-
Interpolates from voxelsSource to voxelsDestination for unsigned 8-bit
buffers.
- interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorImgLib2
-
- interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorNone
-
- interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorRecordExecutionTime
-
- interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorImageJ
-
- interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class InterpolatorOpenCV
-
- interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class Interpolator
-
Interpolates from voxelsSource to voxelsDestination for float buffers.
- interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorImgLib2
-
- interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorNone
-
- interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorRecordExecutionTime
-
- interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorImageJ
-
- interpolateFloat(VoxelBuffer<FloatBuffer>, VoxelBuffer<FloatBuffer>, Extent, Extent) - Method in class InterpolatorOpenCV
-
- InterpolateHelper - Class in org.anchoranalysis.image.voxel.interpolator
-
- interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class Interpolator
-
Interpolates from voxelsSource to voxelsDestination for unsigned 16-bit
buffers.
- interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorImgLib2
-
- interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorNone
-
- interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorRecordExecutionTime
-
- interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorImageJ
-
- interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class InterpolatorOpenCV
-
- Interpolator - Class in org.anchoranalysis.image.voxel.interpolator
-
Copies voxels while performing interpolation.
- Interpolator() - Constructor for class Interpolator
-
- InterpolatorBean - Class in org.anchoranalysis.image.bean.interpolator
-
- InterpolatorBean() - Constructor for class InterpolatorBean
-
- InterpolatorBeanImageJ - Class in org.anchoranalysis.io.imagej.bean
-
- InterpolatorBeanImageJ() - Constructor for class InterpolatorBeanImageJ
-
- InterpolatorBeanOpenCV - Class in org.anchoranalysis.plugin.opencv.bean.interpolate
-
- InterpolatorBeanOpenCV() - Constructor for class InterpolatorBeanOpenCV
-
- InterpolatorFactory - Class in org.anchoranalysis.image.voxel.interpolator
-
Creates instances of
Interpolator to match particular circumstances.
- InterpolatorImageJ - Class in org.anchoranalysis.io.imagej.interpolator
-
- InterpolatorImageJ() - Constructor for class InterpolatorImageJ
-
- InterpolatorImgLib2 - Class in org.anchoranalysis.image.voxel.interpolator
-
Performs interpolation using ImgLib2.
- InterpolatorImgLib2(InterpolatorFactory<UnsignedByteType, RandomAccessible<UnsignedByteType>>, InterpolatorFactory<UnsignedShortType, RandomAccessible<UnsignedShortType>>, InterpolatorFactory<FloatType, RandomAccessible<FloatType>>) - Constructor for class InterpolatorImgLib2
-
- InterpolatorImgLib2Lanczos - Class in org.anchoranalysis.image.voxel.interpolator
-
- InterpolatorImgLib2Lanczos() - Constructor for class InterpolatorImgLib2Lanczos
-
Default constructor.
- InterpolatorImgLib2Linear - Class in org.anchoranalysis.image.voxel.interpolator
-
- InterpolatorImgLib2Linear() - Constructor for class InterpolatorImgLib2Linear
-
Default constructor.
- InterpolatorImgLib2NearestNeighbor - Class in org.anchoranalysis.image.voxel.interpolator
-
- InterpolatorImgLib2NearestNeighbor() - Constructor for class InterpolatorImgLib2NearestNeighbor
-
Default constructor.
- InterpolatorNone - Class in org.anchoranalysis.image.voxel.interpolator
-
Doesn't do any interpolation, just copies a single value for each voxel.
- InterpolatorNone() - Constructor for class InterpolatorNone
-
- InterpolatorOpenCV - Class in org.anchoranalysis.plugin.opencv.interpolator
-
Interpolates using OpenCV's cv2.resize function.
- InterpolatorOpenCV() - Constructor for class InterpolatorOpenCV
-
- InterpolatorRecordExecutionTime - Class in org.anchoranalysis.image.voxel.interpolator
-
- InterpolatorRecordExecutionTime(Interpolator, ExecutionTimeRecorder, String) - Constructor for class InterpolatorRecordExecutionTime
-
- intersect(ObjectMask, Extent) - Method in class ObjectMask
-
Intersects this object-mask with another
- IntersectingCircleObjectsFixture - Class in org.anchoranalysis.test.feature.plugins.objects
-
- IntersectingObjects<T> - Class in org.anchoranalysis.image.voxel.object
-
A data-structure to efficiently determine which object-masks intersect in a collection.
- IntersectingObjects(Collection<T>, Function<T, ObjectMask>) - Constructor for class IntersectingObjects
-
Creates an r-tree for particular objects, as extracted from elements.
- Intersection - Class in org.anchoranalysis.plugin.image.bean.object.match
-
- Intersection() - Constructor for class Intersection
-
- Intersection - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair
-
Finds the intersection of two objects and calculates a feature on it
- Intersection() - Constructor for class Intersection
-
- intersection() - Method in class BoundingBox
-
For evaluating the intersection between this bounding-box and others.
- IntersectionOverUnion - Class in org.anchoranalysis.spatial.box
-
- intersectsWith(ObjectMask) - Method in class IntersectingObjects
-
All elements that intersect with a particular object.
- intersectsWith(BoundingBox) - Method in class IntersectingObjects
-
All elements that intersect with a particular bounding box.
- IntersectsWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Keeps objects which intersects with ANY ONE of a collection of other objects.
- IntersectsWith() - Constructor for class IntersectsWith
-
- intersectsWith(BoundingBox) - Method in class BoundingBoxRTree
-
Which bounding-boxes intersect with another specific bounding box?
- intersectsWith(double, double) - Method in class IntervalRTree
-
Which bounding-boxes intersect with another specific bounding box?
- IntersectsWithContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
-
Returns only the objects that intersect with at least one object in the container
- IntersectsWithContainer() - Constructor for class IntersectsWithContainer
-
- intersectsWithStream(ObjectMask) - Method in class IntersectingObjects
-
- intersectsWithStream(BoundingBox) - Method in class BoundingBoxRTree
-
- intersectsWithStream(double, double) - Method in class IntervalRTree
-
- intersectsWithStream(Rectangle) - Method in class RTree
-
A stream of the elements that a rectangle intersects with.
- intersectWith(Extent) - Method in class Extent
-
Intersects this extent with another (i.e.
- IntervalRTree<T> - Class in org.anchoranalysis.spatial.rtree
-
An R-Tree that contains items, each with an associated one-dimensional interval.
- IntervalRTree() - Constructor for class IntervalRTree
-
Creates an empty R-Tree.
- IntervalRTree(int) - Constructor for class IntervalRTree
-
Creates an empty R-Tree with a specified number of children.
- intFromDouble(Point3d, boolean) - Static method in class PointConverter
-
- intFromDoubleCeil(Point3d) - Static method in class PointConverter
-
- intFromDoubleFloor(Point2d) - Static method in class PointConverter
-
- intFromDoubleFloor(Point3d) - Static method in class PointConverter
-
- intFromFloat(Point3f, boolean) - Static method in class PointConverter
-
- IntToFloatFunction - Interface in org.anchoranalysis.core.functional.unchecked
-
Represents a function that accepts an int-valued argument and produces a float-valued result.
- INVALID_AXIS_INDEX - Static variable in class AxisConverter
-
Human-readable error message used when an invalid int-value for axis is
passed.
- INVALID_AXIS_STRING - Static variable in class AxisConverter
-
Human-readable error message used when an invalid
String-value for
axis is
passed.
- invalidate() - Method in interface FeatureCalculationCache
-
Invalidates existing caches so the next calculation occurs freshly.
- invalidate() - Method in interface ResettableCalculation
-
Resets the cached-calculation, so the next call to doOperationWithParameters() is guaranteed
to calculation the operation, and store the value in the cache.
- invalidate() - Method in class CalculationPart
-
- invalidate() - Method in class CalculationPartMap
-
Invalidates the cache, removing any items already stored.
- invalidateExcept(Set<ChildCacheName>) - Method in interface FeatureCalculationCache
-
Invalidates existing caches so the next calculations occur freshly - except some particular
child-caches who are not invalidated.
- InvalidPathArgumentException - Exception in org.anchoranalysis.launcher.executor.selectparam.path.convert
-
An exception throw if an invalid-path is inputted as an argument.
- InvalidPathArgumentException(String) - Constructor for exception InvalidPathArgumentException
-
- InvalidPathArgumentException(String, InvalidPathException) - Constructor for exception InvalidPathArgumentException
-
- invert(Mask) - Static method in class MaskInverter
-
Modifies a mask so that off voxels become on voxels and vice versa.
- invert() - Method in class BinaryVoxels
-
Changes the off state to be the on state and vice-versa.
- invert() - Method in class BinaryValuesByte
-
Inverts the values so off becomes on, and vice-versa.
- invert() - Method in class ObjectMask
-
Produces a new object-mask that uses the same voxel-buffer but switches the off and
on mapping.
- Invert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Subtracts each voxel from the maximum value for the channel's data type (e.g.
- Invert() - Constructor for class Invert
-
- Invert - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
Switches on voxels to off and vice-versa.
- Invert() - Constructor for class Invert
-
- Invert - Class in org.anchoranalysis.plugin.image.bean.scale
-
Invert the
ScaleFactor calculated by the
scaleCalculator delegate.
- Invert() - Constructor for class Invert
-
- Invert - Class in org.anchoranalysis.plugin.image.bean.segment.binary
-
Performs a segmentation and inverts and on and off bytes
- Invert() - Constructor for class Invert
-
- invert() - Method in class ScaleFactor
-
Build a new scale factor where each dimension is set to the reciprocal of its current value.
- InvertedMax<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.
- InvertedMax() - Constructor for class InvertedMax
-
- invertObjectDuplicate(ObjectMask) - Static method in class MaskInverter
-
Creates a new object-mask where off voxels become on voxels and vice versa.
- isAcceptDirectoryErrors() - Method in class SearchDirectory
-
If true, continues when a directory-access-error occurs (logging it), otherwise throws an
exception.
- isAccepted() - Method in class DualMarksAnnotation
-
Whether the the annotation was marked as accepted by the annotator?
- isAccepted() - Method in class KernelDecision
-
- isAccepted() - Method in class Reporting
-
- isAcceptMissingResolution() - Method in class WithResolutionBase
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
- isAcceptMissingResolution() - Method in class VoxelPhysicalSize
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
- isAcceptNoResolution() - Method in class ReadVoxelExtentXml
-
If false, an exception is thrown if the resolution file is missing for a particular image.
- isAcceptOutsideScene() - Method in class CheckMarkWithMask
-
- isAddName() - Method in class CombineCSV
-
- isAddOne() - Method in class Quantile
-
- isAlways2D() - Method in class StackWriteAttributes
-
Whether the output is guaranteed to only ever 2D i.e.
- isApplyResolution() - Method in class DistanceTransform3D
-
Multiples the values by the x-resolution, if it exists.
- isApplyToPath() - Method in class MatchRegularExpression
-
If true, the filter is applied to the path as a whole, not just the filename (using forward
slashes as directory separators)
- isAsPercentage() - Method in class Quantile
-
If true, the quantile is interpreted as a percentage rather than a decimal
- isAtLeastOnePositive() - Method in class MorphologicalIterations
-
Checks that at least one of iterationsDilation and iterationsErosion is more
than 0
- isAvoidBulletOnFirst() - Method in class SummarizerAggregate
-
Iff true no bullet is added for the very first-item in the list
- isAvoidDivideByZero() - Method in class Divide
-
- isAvoidOverlappingObjects() - Method in class PairNeighbors
-
If true, no overlapping objects are treated as pairs
- isBest() - Method in class Reporting
-
- isBest() - Method in class VoxelizedMarksChangeReporter
-
- isBigNeighborhood() - Method in class Dilate
-
- isBigNeighborhood() - Method in class ConnectedComponentsFromMask
-
If true uses 8 neighborhood rather than 4 neighborhood etc.
- isBigNeighborhood() - Method in class DecomposeIntoConnectedComponents
-
if true, uses 8 neighborhood instead of 4, and similarly in 3d
- isBigNeighborhood() - Method in class Dilate
-
- isBigNeighborhood() - Method in class TraverseOuterContourOnImage
-
- isBinary() - Method in class StackWriteAttributes
-
Whether all channels represent a binary image.
- isBinary() - Method in class ScaleImage
-
Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling
ensures only two binary-values are ouputted.
- isBit0() - Method in class RegionMembership
-
- isBit1() - Method in class RegionMembership
-
- isBit2() - Method in class RegionMembership
-
- isBit3() - Method in class RegionMembership
-
- isBit4() - Method in class RegionMembership
-
- isBit5() - Method in class RegionMembership
-
- isBit6() - Method in class RegionMembership
-
- isBit7() - Method in class RegionMembership
-
- isBold() - Method in class TextStyle
-
Whether to bold the drawn text
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderBase
-
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderXY
-
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class AtBorderZ
-
- isBufferOff(UnsignedByteBuffer) - Method in class KernelPointCursor
-
Is the value at the current index in this buffer corresponding to an off state?
- isBufferOn(UnsignedByteBuffer) - Method in class KernelPointCursor
-
Is the value at the current index in this buffer corresponding to an on state?
- isBySlices() - Method in class ConnectedComponentsFromMask
-
- isCalledRegisterAllPackage() - Static method in class RegisterBeanFactories
-
- isCaseSensitive() - Method in class PatternSpan
-
Iff true, a case sensitive search is used to match patterns.
- isCellUsed(int, int) - Method in class TableItemArrangement
-
- isChangeExisting() - Method in class ConvertBase
-
If true, the existing channel can be changed.
- isClearOutsideMask() - Method in class ThresholdAgainstChannel
-
- isCollapseFilename() - Method in class FilePathAppendBase
-
- isCompatibleWith(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class FeatureInputType
-
Can these parameters be used with a particular feature?
- isCompatibleWith(Mark) - Method in interface CompatibleWithMark
-
- isCompatibleWith(Mark) - Method in class AndList
-
- isCompatibleWith(Mark) - Method in class CheckMarkWithMask
-
- isCompatibleWith(Mark) - Method in class FeatureValueCheckMark
-
- isCompatibleWith(Mark) - Method in class Not
-
- isCompatibleWith(Mark) - Method in class RadiiMinRatio
-
- isCompatibleWith(Mark) - Method in class VolumeMin
-
- isCompatibleWith(Mark) - Method in class CreateNew
-
- isCompatibleWith(Mark) - Method in class FromMarkProposer
-
- isCompatibleWith(Mark) - Method in class FromObjects
-
- isCompatibleWith(Mark) - Method in class FromProvider
-
- isCompatibleWith(Mark) - Method in class FromSerializedMarks
-
- isCompatibleWith(Mark) - Method in class Check
-
- isCompatibleWith(Mark) - Method in class Check
-
- isCompatibleWith(Mark) - Method in class MarkFromCollectionProposerUnary
-
- isCompatibleWith(Mark) - Method in class UniformRandom
-
- isCompatibleWith(Mark) - Method in class FromSerializedObject
-
- isCompatibleWith(Mark) - Method in class MarkProposerFromList
-
- isCompatibleWith(Mark) - Method in class MarkProposerReference
-
- isCompatibleWith(Mark) - Method in class MarkProposerUnary
-
- isCompatibleWith(Mark) - Method in class ObjectAsPoints
-
- isCompatibleWith(Mark) - Method in class OrientationAndRadiiProposer
-
- isCompatibleWith(Mark) - Method in class Position
-
- isCompatibleWith(Mark) - Method in class MarkMergeProposerReference
-
- isCompatibleWith(Mark) - Method in class MergeMarkEllipse
-
- isCompatibleWith(Mark) - Method in class RandomOrientation
-
- isCompatibleWith(Mark) - Method in class RandomXY
-
- isCompatibleWith(Mark) - Method in class IncludeRandomObjects
-
- isCompatibleWith(Mark) - Method in class XYOrientationExtendToZ
-
- isCompatibleWith(Mark) - Method in class RadiiProposerRepeat
-
- isCompatibleWith(Mark) - Method in class UniformRandomRadiiProposer
-
- isCompatibleWith(Mark) - Method in class MarkSplitProposerReference
-
- isCompatibleWith(Mark) - Method in class KernelBirthPartition
-
- isCompatibleWith(Mark) - Method in class KernelReplacePartition
-
- isCompatibleWith(Mark) - Method in class KernelBirthAndKill
-
- isCompatibleWith(Mark) - Method in class KernelDeath
-
- isCompatibleWith(Mark) - Method in class KernelExchange
-
- isCompatibleWith(Mark) - Method in class KernelInitialMarksFromPartition
-
- isCompatibleWith(Mark) - Method in class KernelInitialMarksProposed
-
- isCompatibleWith(Mark) - Method in class KernelInitialMarksVoxelized
-
- isCompatibleWith(Mark) - Method in class KernelMerge
-
- isCompatibleWith(Mark) - Method in class KernelSplit
-
- isCompatibleWith(Mark) - Method in class KernelBirthVoxelized
-
- isCompatibleWith(Mark) - Method in class ConstantWeight
-
- isCompatibleWith(Mark) - Method in class NumberPoints
-
- isCompatibleWith(Mark) - Method in class FitPoints
-
- isCompatibleWith(Mark) - Method in class LinearLeastSquaresEllipseFitter
-
- isCompatibleWith(Mark) - Method in class LinearLeastSquaresEllipsoidFitter
-
- isCompatibleWith(Mark) - Method in class Reference
-
- isCompatibleWith(Mark) - Method in class ReflectInAxesWithinDistance
-
- isCompleted() - Method in class JobState
-
- isCompletedFailure() - Method in class JobState
-
- isCompletedSuccessfully() - Method in class JobState
-
- isConditionTrue() - Method in class DictionaryCondition
-
- isConnectedComponentID(int) - Method in class EncodedIntBuffer
-
- isConnectedComponentIDCode(int) - Method in class EncodedVoxels
-
- isConnectedComponentIDCode(int) - Method in class WatershedEncoding
-
- isConsiderForMerge() - Method in class PrioritisedVertex
-
- isConvexHull() - Method in class FitPointsFromObjects
-
If true, Reduces the set of points by applying a convex-hull operation
- isCopyNonInputs() - Method in class InputArguments
-
If True, any files in the input directory that are unused as inputs, are copied to the output
directory.
- isCov() - Method in class ObjectRadiusStandardDeviation
-
- isCreateShort() - Method in class ArrangeRaster
-
- isCreateShort() - Method in class GenerateString
-
- isCreateShort() - Method in class TileWithLabels
-
- isCreateShort() - Method in class DistanceTransform3D
-
- isCreateShort() - Method in class DistanceTransformForEachObject3D
-
- isCreateShort() - Method in class CreateNew
-
If True creates an unsigned short-image
- isCsvIgnoreZeros() - Method in class ExportImageHistograms
-
Iff true, bins with zero-counts are not written as a row in the CSV file.
- isDatasetNameSubdirectory() - Method in class ExperimentResultsExperimentStructure
-
If true the datasetName is appended as a subdirectory e.g.
- isDay() - Method in class ExperimentIdentifierAuto
-
If true, the current day (yyyy.MM.dd) is included in the output
- isDebug() - Method in class RootPath
-
If true this root is preferred, when executing a job in debugging mode.
- isDebug() - Method in class ThresholdedFeature
-
- isDebugEnabled() - Method in class InputOutputContextStateful
-
- isDebugEnabled() - Method in interface InputOutputContext
-
Is debug-mode enabled?
- isDebugEnabled() - Method in class OptimizationContext
-
- isDebugMode() - Method in class PathPrefixerContext
-
Whether debug-mode is activated.
- isDebugModeActivated() - Method in class InputManagerParameters
-
- isDebugModeEnabled() - Method in class ExecutionArguments
-
- isDefault() - Method in interface SelectParam
-
Is this the default option that occurs without any additional user effort?
- isDefault() - Method in class UseDefaultManager
-
- isDetailedLogging() - Method in class ExperimentFeedbackContext
-
Iff true, additional log messages are written to describe each job in terms of its unique
name, output folder, average execution time etc.
- isDetailedLogging() - Method in class InputBound
-
- isDetailedLogging() - Method in class ParametersExperiment
-
Iff true, additional log messages are written to describe each job in terms of its unique
name, output folder, average execution time etc.
- isDifferentColorsForPairs() - Method in class AssignmentColorPool
-
If true, different colors are used for paired objects, otherwise always the same color is
used.
- isDirect() - Method in class UnsignedBuffer
-
Is this buffer direct or non-direct?
- isDirect() - Method in class VoxelBuffer
-
Is this buffer direct or non-direct?
- isDirect() - Method in class VoxelBufferUnsigned
-
- isDirectionChainCode(int) - Method in class EncodedVoxels
-
- isDirectionChainCode(int) - Method in class WatershedEncoding
-
- isDisableDebugMode() - Method in class RootedFilePath
-
- isDisableDebugMode() - Method in class Rooted
-
- isDo3D() - Method in class AnisotropicDiffusion
-
Whether to perform the diffusion in 3D direction, or rather only in the 2D plane.
- isDo3D() - Method in class ObjectCollectionProviderMorphological
-
- isDo3D() - Method in class MorphologicalIterations
-
Whether to perform the morphological dimensions in 3D or 2D
- isDo3D() - Method in class PairNeighbors
-
- isDo3D() - Method in class TouchingVoxels
-
- isDo3D() - Method in class Erode
-
- isDo3D() - Method in class NumberRemovedVoxelsAfterClosing
-
- isDo3D() - Method in class OutlineKernelBase
-
- isDo3D() - Method in class UniformRandomRadiiProposer
-
- isDrawReverseLine() - Method in class Orientation
-
- isDuplicate() - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting existing data
This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- isDuplicate() - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting
data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- isEightBitChannels() - Method in class StackWriteAttributes
-
Whether each channel is 8 bits.
- isEmpty() - Method in class DoubleList
-
- isEmpty() - Method in class DoubleSet
-
- isEmpty() - Method in class IntegerList
-
- isEmpty() - Method in class IntegerSet
-
- isEmpty() - Method in interface PrimitiveBeanCollection
-
Whether the collection is empty or not.
- isEmpty() - Method in class StringList
-
- isEmpty() - Method in class StringSet
-
- isEmpty() - Method in class MapCreate
-
Whether the map is empty or not.
- isEmpty() - Method in interface NamedProvider
-
Are there any items in the provider?
- isEmpty() - Method in class RecordedExecutionTimes
-
Are there no recorded operations?
- isEmpty() - Method in class FeatureList
-
Returns true if this list contains no elements.
- isEmpty() - Method in class ResultsVectorList
-
Returns true if the list contains no elements.
- isEmpty() - Method in class TimeSequence
-
- isEmpty() - Method in class ObjectCollection
-
Whether the collection contains no objects.
- isEmpty() - Method in class InputsWithDirectory
-
- isEmpty() - Method in class RecordedOutputs
-
If no output-names exist.
- isEmpty() - Method in class Histogram
-
If no value exists in the histogram with a count greater than zero.
- isEmpty() - Method in class UpdatableMarksList
-
- isEmpty() - Method in class MarkCollection
-
- isEmpty() - Method in class Extent
-
Does the extent contain zero voxels?
- isEmpty() - Method in class PointRange
-
Has a valid min and max defined?
- isEmpty() - Method in class RTree
-
Returns true if and only if the R-tree is empty of entries.
- isEnabled() - Method in class TextFileOutput
-
- isErodeAtBoundary() - Method in class ConvexHullBase
-
- isErrorDisconnectedObjects() - Method in class RemoveIntersectingVoxels
-
If true, throws an error if there is a disconnected object after the erosion
- isEvaluated() - Method in class CachedSupplierBase
-
Has the function already been evaluated?
- isExceptionIfEmpty() - Method in class FeatureHistogramStatistic
-
If true, then an exception is thrown if the histogram is empty, otherwise
is returned.
- isExcludeZero() - Method in class Intensity
-
Iff true, zero-valued voxels are excluded from the histogram
- isExcludeZero() - Method in class IntensityMeanMaxSlice
-
- isExcludeZero() - Method in class Intensity
-
If true, zeros are excluded from considering in the histogram
- isExecuting() - Method in class JobState
-
- isExitBeforeOptimization() - Method in class SegmentWithMarkedPointProcess
-
Iff true the algorithm exits before optimization begins (useful for debugging).
- isExitWithMinima() - Method in class WatershedYeong
-
If true, exits early and just returns the minima, without any further segmentation
- isExpandLabelZ() - Method in class TileWithLabels
-
- isExtendInZ() - Method in class ExportObjectsAsCroppedImages
-
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all
slices)
- isFieldAnnotatedAsOptional(Field) - Static method in class FieldAccessor
-
- isFindMaxima() - Method in class ExtractSlice
-
If true, the maxima of the score is searched for.
- isFinished() - Method in class DualMarksAnnotation
-
- isFirst() - Method in class AsSingle
-
Iff true, first object is used, otherwise the second
- isFirstDefined() - Method in class OutputEnableRulesSpecify
-
- isFirstLineHeaders() - Method in class CombineCSV
-
- isFixRandomSeed() - Method in class SegmentWithMarkedPointProcess
-
Iff true uses a constant seed for the random-number-generator (useful for debugging).
- isFlatten() - Method in class MultipleComparer
-
If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane,
before comparison.
- isFlatten() - Method in class CompareAnnotations
-
If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane,
before comparison.
- isFlatten() - Method in class ExteriorContour
-
If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make
it 2D
- isFlatten() - Method in class ColoredBase
-
If true, objects and the background are flattened in the z dimension (via maximum intensity
projection), so that a 2D image is produced.
- isForceChangeBytes() - Method in class Invert
-
If true, rather than modifying the binary-values (an index) bytes are modified in the buffer
to reflect the existing binary-values.
- isForceDetailedLogging() - Method in class OutputExperiment
-
Whether more detailed log-messages around each experiment occur.
- isForceEagerEvaluation() - Method in class NamedChannelsAppend
-
- isForceRGB() - Method in class ArrangeRaster
-
If set, ensures every stack is converted into 3 channels
- isForwardDirectionOnly() - Method in class XYOrientationExtendToZ
-
- isGaussian() - Method in class AddEdgeFilters
-
If true, the Gaussian filter is included
- isHighestTwoRadiiOnly() - Method in class RadiiRatio
-
- isIgnoreAtThreshold() - Method in class OutlineKernelBase
-
- isIgnoreCase() - Method in class FilePathPattern
-
if true, case is ignored in the pattern matching.
- isIgnoreFileNotFoundAppend() - Method in class NamedChannelsAppend
-
- isIgnoreFittingFailure() - Method in class FitPointsFromObjects
-
If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply
not included (with only a log error) If false, an exception is thrown
- isIgnoreHidden() - Method in class SearchDirectory
-
If true, case is ignored in the pattern matching.
- isIgnoreHidden() - Method in class FilePathPattern
-
Iff true, any hidden-path is not considered, and simply ignored
- isIgnoreHigherSide() - Method in class GaussianCumulative
-
- isIgnoreLowerSide() - Method in class GaussianCumulative
-
- isIgnoreMissingChannel() - Method in class IndependentChannels
-
Iff true and we cannot find a channel in the file, we ignore it and carry on
- isIgnoreNaN() - Method in class Sum
-
If true, we ignore any NaN values.
- isIgnoreNoObjects() - Method in class SegmentInstanceWithModel
-
If true, then the outputs (outline, mask, image etc.) are not written for images that produce
no objects.
- isIgnoreOutside() - Method in class KernelApplicationParameters
-
When true, any parts of the neighborhood that lie outside the scene are not considered in
kernel neighborhoods.
- isIgnoreOutside() - Method in enum OutsideKernelPolicy
-
When true, any parts of the neighborhood that lie outside the scene are not considered in
kernel neighborhoods.
- isIgnoreRangeAxisOutside() - Method in class LinePlot
-
- isIgnoreZero() - Method in class RatioNonMode
-
- isIgnoreZeros() - Method in class HistogramCSVGenerator
-
Iff true bins in the histogram with a zero count are not written
- isIgnoreZIfNaN() - Method in class DistanceTransform3D
-
If the z-resolution is undefined, the z dimenion is ignored.
- isIncludeBatchDimension() - Method in class SegmentObjectsFromONNXModel
-
If true, a 4-dimensional tensor is created (with the first dimension describing a batch-size
of 1), instead of the usual 3-dimensional tensor describing channel, height, width.
- isIncludeDirectories() - Method in class DirectoryStructure
-
If false, the folders are ignored, and only the file-name is used in the output
- isIncludeFeatureNames() - Method in class EnergySchemeCreatorByElement
-
If true, the names of the imageFeatures are taken as a combination of the namedItem and the
actual features
- isIncludeFileName() - Method in class AppendDictionary
-
- isIncludeFirst() - Method in class PairNeighbors
-
Include features for the First-object of the pair
- isIncludeMerged() - Method in class PairNeighbors
-
Include features for the Merged-object of the pair
- isIncludeSecond() - Method in class PairNeighbors
-
Include features for the Second-object of the pair
- isIncludeShell() - Method in class MaxOverlapRatio
-
- isIncludeZ() - Method in class Outline
-
If true the outline is also applied in the z-dimension, otherwise this is ignored as possible
boundary
- isIncludeZ() - Method in class NotTouchingSceneBorder
-
- isInitialized() - Method in class InitializableBean
-
- isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class JobProcessor
-
Is an input-object compatible with this particular task?
- isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class Task
-
Is an input-object compatible with this particular task?
- isInteger() - Method in class FloatVoxelType
-
- isInteger() - Method in class SignedVoxelType
-
- isInteger() - Method in class UnsignedVoxelType
-
- isInteger() - Method in class VoxelDataType
-
Whether the data-type represents an integer or floating-point?
- isInterleaveChannels() - Method in class SegmentObjectsFromONNXModel
-
If true, the channels are placed as the final position of the tensor (**after** width/height)
instead of **before** width/height.
- isInterleaved() - Method in class ImageFileEncoding
-
Whether the channels are interleaved
- isInterpolate() - Method in class AtScale
-
- isInverse() - Method in class IntersectsWithContainer
-
- isInverse() - Method in class IntensityMeanShellBase
-
Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is
removed).
- isInverseMask() - Method in class IntensityMeanShellBase
-
If true, uses the inverse of the passed mask.
- isInvert() - Method in class MaskAsObject
-
- isInvert() - Method in class FromObjects
-
- isInvert() - Method in class FilterWithRegularExpression
-
Iff true, then a file is rejected if the regular-expression matches and vice-versa.
- isInvertDecisionValue() - Method in class FeatureListProviderSVMClassifier
-
- isItemIncluded(T) - Method in class Plot
-
Whether to include this particular item in the plot?
- isKeepEntireImage() - Method in class ExportObjectsAsCroppedImages
-
If true, rather than writing out a bounding-box around the object-mask, the entire image is
written
- isKeepExtremes() - Method in class Identity
-
- isKeepZ() - Method in class ImposeResolution
-
Keep the z-resolution if it is already defined
- isKeyRequired() - Method in class RegularExpression
-
- isLabel() - Method in class MontageSlices
-
If true a label is added beside every image showing the slice index
- isLeaf() - Method in class ErrorNodeImpl
-
- isLocalized() - Method in class FilesProviderWithDirectoryString
-
- isLogPath() - Method in class Rooted
-
if true, the pathIn and pathOut are logged.
- isMarksSpan(MarkCollection) - Method in class RandomCollectionWithAddCriteria
-
- isMarksSpan() - Method in class VoxelizedMarksWithEnergy
-
- isMarksSpan(MarkCollection) - Method in class EnergySavedPairs
-
- isMax() - Method in class IdentityImposeValueRelationToHistogram
-
- isMedian() - Method in class AddEdgeFilters
-
If true, the median filter is included
- isMemberFlag(byte, byte) - Method in class RegionMembership
-
- isMemberFlag(byte, byte) - Method in class RegionMembershipAnd
-
- isMemberFlag(byte, byte) - Method in class RegionMembershipOr
-
- isMemberFlag(byte) - Method in class RegionMembershipWithFlags
-
- isMemberFlagAnd(byte, byte) - Static method in class RegionMembershipUtilities
-
- isMemberFlagOr(byte, byte) - Static method in class RegionMembershipUtilities
-
- isMerge() - Method in class CutBelowThreshold
-
- isMinima(int) - Method in class EncodedIntBuffer
-
- isMinima(int) - Method in class EncodedVoxels
-
- isMip() - Method in class NumberVoxels
-
- isMip() - Method in class SurfaceNumberVoxelsBase
-
- isMip() - Method in class OverlapMIPBase
-
- isNoBlack() - Method in class ThresholderAutoIJ
-
- isNormalize() - Method in class Identity
-
- isNormalize() - Method in class BoundingBoxZOverlapRatio
-
- isNormalizeFeatures() - Method in class FeatureListProviderSVMClassifier
-
Normalize features
- isNoScale() - Method in class ScaleFactor
-
Does the scale-factor involve no scaling at all?
- isNumeric() - Method in class TypedValue
-
Whether the value is numeric or not.
- isNumeric() - Method in class ReportFeature
-
- isNumeric() - Method in class ReportFeatureOnMark
-
- isNumeric() - Method in class ReportFeatureOnMarks
-
- isNumeric() - Method in class ReportFeatureOnObjectsBase
-
- isNumeric() - Method in class ReportFeatureWrapError
-
- isNumeric() - Method in class NumberMarksFromManifest
-
- isNumeric() - Method in class ReportFeatureForManifestFileBase
-
- isNumeric() - Method in class RootFilePathRegEx
-
- isOff(int, int, int) - Method in interface BinaryOnOffSetter
-
Does the voxel at this point have an off state?
- isOff(Point3i) - Method in interface BinaryOnOffSetter
-
Does the voxel at this point have an off state?
- isOff(byte) - Method in class BinaryValuesByte
-
Does a particular value correspond to the off state?
- isOmitExperimentIdentifier() - Method in class OutputArguments
-
- isOmitExperimentIdentifier() - Method in class OutputPrefixerSettings
-
Requests that the experiment-identifier (name and index) is not included in the
output-directory path.
- isOn(int, int, int) - Method in interface BinaryOnOffSetter
-
Does the voxel at this point have an on state?
- isOn(Point3i) - Method in interface BinaryOnOffSetter
-
Does the voxel at this point have an on state?
- isOn(byte) - Method in class BinaryValuesByte
-
Does a particular value correspond to the on state?
- isOn() - Method in interface OutputSequence
-
- isOn() - Method in class OutputSequenceIncrementing
-
- isOn() - Method in class OutputSequenceIndexed
-
- isOpenInDesktop() - Method in class ExperimentExecutor
-
Whether to open the output directory in the desktop GUI after execution (if supported on the
O/S).
- isOperationAlreadyRecorded(String) - Method in class ExecutionTimeRecorder
-
Has a particular operation already been recorded?
- isOperationAlreadyRecorded(String) - Method in class ExecutionTimeRecorderIgnore
-
- isOutline() - Method in class ColoredBase
-
If true, an outline is drawn around the entries.
- isOutlineAtBoundary() - Method in class ExteriorContour
-
- isOutputEnabled() - Method in class CSVWriter
-
- isOutputEnabled(String) - Method in class All
-
- isOutputEnabled(String) - Method in class IgnoreUnderscorePrefix
-
- isOutputEnabled(String) - Method in class None
-
- isOutputEnabled(String) - Method in class SpecificDisabled
-
- isOutputEnabled(String) - Method in class SpecificEnabled
-
- isOutputEnabled(String) - Method in class MultiLevelBinary
-
- isOutputEnabled(String) - Method in class MultiLevelNot
-
- isOutputEnabled(String) - Method in class OutputEnabledMutable
-
- isOutputEnabled(String) - Method in class SingleLevelBinary
-
- isOutputEnabled(String) - Method in class SingleLevelInSet
-
- isOutputEnabled(String) - Method in class SingleLevelNot
-
- isOutputEnabled(String) - Method in interface SingleLevelOutputEnabled
-
Is a particular a particular output-enabled?
- isOutputIncrementingNumberSequence() - Method in class OutputPrefixerSettings
-
Requests outputting with an incrementing number sequence, rather than the usual outputter
(normally based upon input filenames).
- isOutputShort() - Method in class GradientBase
-
Iff true, outputs a short channel, otherwise byte channel
- isOutsideAtThreshold() - Method in class OutlineKernelBase
-
- isOutsideOffUnignored() - Method in class KernelApplicationParameters
-
True only when voxels outside the scene should not be ignored and considered as
off.
- isOutsideOffUnignored() - Method in class KernelPointCursor
-
True only when voxels outside the scene should not be ignored and considered as
off.
- isOutsideOn() - Method in class KernelApplicationParameters
-
- isOutsideOn() - Method in class KernelPointCursor
-
Whether to treat voxels that lie outside the scene as on (if true) or off (if
false).
- isOutsideOn() - Method in enum OutsideKernelPolicy
-
- isOutsideOnUnignored() - Method in class KernelApplicationParameters
-
True only when voxels outside the scene should not be ignored and considered as
on.
- isOverlappingObjects() - Method in class OutlinePreserveRelativeSize
-
Whether objects may overlap or not when unscaled.
- isParamPrefixAppendNumber() - Method in class PermuteFirstSecondOrder
-
If true the constant is appended to the param prefix (a dot and a number)
- isPhysical() - Method in class UnitConverter
-
- isPlateau(int) - Method in class EncodedVoxels
-
- isPlayloadUsed() - Method in class MergePairs
-
- isPlayloadUsed() - Method in class MergeToIncreaseObjectFeature
-
- isPlayloadUsed() - Method in class MergeWithFeature
-
Is the payload considered in making decisions? (iff false, payload of nodes is irrelvant)
- isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>) - Static method in class VisitSchedulerConvexAboutRoot
-
- isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>, boolean) - Static method in class VisitSchedulerConvexAboutRoot
-
- isPointInside(Point3i) - Method in class Ellipse
-
- isPointInside(Point3i) - Method in class Ellipsoid
-
- isPointInside(Point3i) - Method in class MarkWithPositionAndSingleRadius
-
- isPointInside(Point3i) - Method in class Mark
-
- isPointInside(Point3i) - Method in class LineSegment
-
- isPointInside(Point3i) - Method in class PointList
-
- isPointInside(Point3i) - Method in class Polygon
-
- isPointInside(Point3i) - Method in class PolygonCurve
-
- isPointInside(Point3i) - Method in class RotatableBoundingBox
-
- isPointInside(DrawOverlay, Point3i) - Method in class OverlayMark
-
- isPointInside(DrawOverlay, Point3i) - Method in class OverlayObjectMask
-
- isPointInside(DrawOverlay, Point3i) - Method in class Overlay
-
Is a point inside an overlay? (for a particular OverlayWriter).
- isPointOnMask(Point3d, EnergyStack, Function<Point3d, Point3i>) - Method in class CheckMarkWithMask
-
- isPrefix() - Method in class FromXMLList
-
If true, a prefix is prepended to the name of each added bean.
- isPreserveAspectRatio() - Method in class FitTo
-
If true, the aspect-ratio is preserved between width and height.
- isPreserveAspectRatio() - Method in class ToDimensions
-
If true, the ratio between x and y is kept constant when scaling.
- isPreserveExtensionIfDuplicate() - Method in class RemoveExtension
-
Keeps the extension if the file-name (without the extension) becomes duplicated with another.
- isPreserveSubdirectories() - Method in class ClusterByTimestamp
-
If true, the entire relative-path is used when copying files into the cluster directory.
- isPrioritizeInputContext() - Method in class MatchExtensions
-
When true, any extensions available in the input-context are prioritized ahead of extensions.
- isProposal() - Method in class VoxelizedMarksPeriodicReporter
-
- isProposed() - Method in class KernelDecision
-
- isRadiusInMeters() - Method in class WithRadiusBase
-
- isReadFromResources() - Method in class SegmentObjectsFromONNXModel
-
When true, rather than reading modelPath from the file-system, it is read from Java
resources on the class-path.
- isRecordedAsEnabled(String) - Method in class RecordedOutputs
-
Is a particular output-name recorded as enabled?
- isRecurseSubfolders() - Method in class MultiFileReader
-
- isRecursive() - Method in class SearchDirectory
-
If true the search is applied recursively over sub-directories.
- isRecursive() - Method in class ExperimentResultsExperimentStructure
-
Whether to apply the search recursively or not
- isRejectIterationIfAllLow() - Method in class Erode
-
- isRejectIterationIfDisconnected() - Method in class Erode
-
- isRelativeForIdentifier() - Method in class InputArguments
-
If true, the entire filename or relative path (excluding extension) is used to determine a
unique identifier.
- isRelativeForIdentifier() - Method in class InputContextParameters
-
If true, the entire filename or relative path (excluding extension) is used to determine a
unique identifier.
- isRelativeToDirectory() - Method in class FileNamerContext
-
If true, the namer should prefer to derive file-names relative to the directory, rather than
only the varying elements in the file-names.
- isRemoveExtension() - Method in class FilePathPattern
-
if true, the extension is removed from paths before finding the pattern.
- isRemoveExtensionInDescription() - Method in class LastDirectories
-
Whether to remove the file-extension from the filename.
- isRemoveNaNColumns() - Method in class ExportFeaturesStyle
-
When true, columns containing all
Double.NaN values are removed before outputting.
- isRemoveNaNColumns() - Method in class FeatureExporterContext
-
When true, columns containing all
Double.NaN values are removed before outputting.
- isRemoveTouchingBorderXY() - Method in class FeatureCostAssigner
-
- isReplaceMatchesWithSolids() - Method in class CompareAnnotations
-
- isReplaceWithMidpoint() - Method in class MergeGreedyToIncreaseObjectFeature
-
- isReportFitterErrors() - Method in class FitPoints
-
- isRequireAllFilesMatch() - Method in class GroupFiles
-
- isRequireBBoxNeighbors() - Method in class MergeWithFeature
-
Requires for any potential merge that the bounding-boxes of the two objects must intersect or
touch
- isRequireTouching() - Method in class MergeWithFeature
-
Requires the object-masks to touch.
- isResultUnusual(double) - Method in class ReplaceInfinity
-
- isResultUnusual(double) - Method in class ReplaceNaN
-
- isResultUnusual(double) - Method in class ReplaceUnusualValue
-
- isRewardHigherSide() - Method in class GaussianCumulative
-
Treat the higher side as if it's the the fill cdf
- isRewardLowerSide() - Method in class GaussianCumulative
-
- isRGB() - Method in class DisplayStack
-
Does the display-stack contain an RGB image?
- isRgb() - Method in class ImageMetadata
-
Whether the image is RGB or not.
- isRGB() - Method in class Stack
-
If true, and the stack has exactly three channels, this stack can be interpreted as a RGB
image.
- isRGB() - Method in interface NamedChannelsForSeries
-
Whether the channels describe an RGB image.
- isRGB() - Method in class NamedChannelsForSeriesConcatenate
-
- isRGB() - Method in class NamedChannelsForSeriesMap
-
- isRGB() - Method in interface OpenedImageFile
-
Whether the image-file has RGB encoded voxels.
- isRGB() - Method in class ScaleableBackground
-
- isRGB(IFormatReader) - Method in class Default
-
- isRGB(IFormatReader) - Method in class ForceBitsPerPixel
-
- isRGB(IFormatReader) - Method in class ForceNumberChannels
-
- isRGB(IFormatReader) - Method in class ForceTimeSeriesToStack
-
- isRGB(IFormatReader) - Method in class ReadOptions
-
Is it an image with three channels (red, green and blue)?
- isRGB(IFormatReader) - Method in class ReadOptionsDelegate
-
- isRGB(IFormatReader) - Method in class SwitchChannelTime
-
- isRgb() - Method in class ImageFileEncoding
-
Whether the source bytes encoded as RGB (i.e.
- isRgb() - Method in class FromChannelOrMask
-
If true, the output contains three channels (the input and two duplicates) instead of one
- isRGB() - Method in class OpenedMultiFile
-
- isRootInStructure() - Method in class ExperimentResultsExperimentStructure
-
If true the directory structure is
ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory
structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
- isScaleLabel() - Method in class TileWithLabels
-
- isSecond() - Method in class ExperimentIdentifierAuto
-
Only relevant if time==true.
- isSecondary() - Method in class VoxelizedMarksPeriodicReporter
-
If proposal is true, this toggles between the primary and secondary proposal
- isSelective() - Method in class OutputPattern
-
Whether the output should be checked to see if it is allowed or not.
- isShowAgg() - Method in class MemoryUsageReporter
-
- isShowBest() - Method in class MemoryUsageReporter
-
- isShowDomainAxis() - Method in class BarPlot
-
- isShowVerticalAxisLines() - Method in class PlotInstance
-
- isShuffle() - Method in class InputArguments
-
If true, the order of the inputs are shuffled (randomized).
- isShuffle() - Method in class InputContextParameters
-
If true, the order of the inputs are shuffled (randomized).
- isSigmaInMeters() - Method in class BlurStrategy
-
- isSilentlyDeleteExisting() - Method in class OutputManager
-
Whether to silently first delete any existing output at the intended path, or rather throw an
error.
- isSingleChannel() - Method in class StackWriteAttributes
-
The number of channels is guaranteed to be 1 in the output.
- isSkipAtBorder() - Method in class FillHoles
-
If true we do not fill any objects that touch the border
- isSkipFileName() - Method in class LastDirectories
-
Iff true the filename is not considered, only the subdirectories.
- isSkipFileName() - Method in class FilePathAppendBase
-
- isSkipMissingChannels() - Method in class NamedChannelsAppend
-
- isSlicesSeparately() - Method in class FitBoxToOnVoxels
-
- isStackAsChannel() - Method in class MultiInputManagerQuick
-
If true, a raster-stack is treated as a single-channel, even if multiple exist (and no
additionalChannel is set)
- isStackBackground() - Method in class VisualizeOnBackground
-
- isStrongEdgeEnhancer() - Method in class AnisotropicDiffusion
-
If true uses, the strong-edge-enhancer diffusion function, otherwise the wide-region-enhancer.
- isSubtractFromMaskOnly() - Method in class SubtractMean
-
- isSuppress3D() - Method in class MorphologicalOperatorBase
-
- isSuppress3D() - Method in class SurfaceNumberVoxelsBase
-
- isSuppress3D() - Method in class SegmentThresholdAboveMinBound
-
- isSuppressDirectories() - Method in class FromDescriptiveName
-
If true, any directory separators in the identifier in a descriptive-name are replaced by
underscores.
- isSuppressErrors() - Method in class ExportFeaturesStyle
-
When false, an image is reported as errored, if any exception is thrown during calculation.
- isSuppressErrors() - Method in class FeatureCalculationContext
-
When false, an image is reported as errored, if any exception is thrown during calculation.
- isSuppressErrors() - Method in class FeatureExporterContext
-
If false, an image is reported as errored, if any exception is thrown during calculation.
- isSuppressErrors() - Method in class FromObjects
-
When true, exceptions aren't thrown when feature-calculations fail, but rather a log error
message is written.
- isSuppressExceptions() - Method in class JobProcessor
-
- isSuppressExceptions() - Method in class ParametersUnbound
-
- isSuppressExceptions() - Method in class QuickMultiDatasetExperiment
-
- isSuppressExceptions() - Method in class QuickMultiDatasetStructuredExperiment
-
- isSuppressOutlineZ() - Method in class ColoredBase
-
if true, the outline is suppressed in the z-dimension i.e.
- isSuppressRes() - Method in class RadiiRatio
-
- isSuppressRootOut() - Method in class Rooted
-
if true, the root is not added to the outFilePath, and the path is instead localized against
the location of the BeanXML.
- isSuppressSeries() - Method in class ConvertImageFormat
-
If true, the series index is not included in the outputted file-names.
- isSuppressSubfolders() - Method in class DefineOutputter
-
- isSuppressZ() - Method in class BoundingBoxIntersection
-
- isSuppressZ() - Method in class DistanceTransform3D
-
- isSuppressZ() - Method in class DistanceTransformForEachObject3D
-
- isSuppressZ() - Method in class MergeWithOptionalDistanceConstraint
-
- isSuppressZ() - Method in class CostOverlapWithinMidpointDistance
-
- isSuppressZ() - Method in class ImageMomentsBase
-
If true co-voariance is suprpessed in z-dimension
- isSuppressZ() - Method in class CenterOnMask
-
- isSuppressZ() - Method in class UniformRandom
-
- isSuppressZ() - Method in class SurfaceSizeMaskNonZero
-
- isSuppressZ() - Method in class EllipsoidBase
-
Iff true, surpresses covariance in the z-direction.
- isSuppressZCovariance() - Method in class FromObjects
-
- isSuppressZCovariance() - Method in class LinearLeastSquaresEllipsoidFitter
-
- isTemporary(int) - Method in class EncodedIntBuffer
-
- isTemporary(int) - Method in class EncodedVoxels
-
- isThreeChannels() - Method in class StackWriteAttributes
-
The number of channels is guaranteed to be 3 in the output.
- isThrowExceptionForInsufficientPoints() - Method in class CreateMarkFromPoints
-
- isThumbnailsEnabled() - Method in class FeatureCalculationContext
-
- isTime() - Method in class ExperimentIdentifierAuto
-
If true, the current time (HH.mm.ss) is included in the output
- isTransposed() - Method in class CombineCSV
-
- isTrue(ObjectWithProperties, RGBStack, int) - Method in interface IfElse.Condition
-
- isUnchanged(double, int) - Method in class UnchangedBase
-
Whether the current value is unchanged compared to the previous value.
- isUnchanged(double, int) - Method in class UnchangedScore
-
- isUnchanged(double, int) - Method in class UnchangedSize
-
- isUniformlySized() - Method in class StackNotUniformSized
-
Do all channels have identical dimensions?
- isUniformTyped() - Method in class StackNotUniformSized
-
Do all
Channels in the stack have identical voxel data-type?
- isUnsigned() - Method in class FloatVoxelType
-
- isUnsigned() - Method in class SignedVoxelType
-
- isUnsigned() - Method in class UnsignedVoxelType
-
- isUnsigned() - Method in class VoxelDataType
-
Whether the data-type is unsigned?
- isUnstarted() - Method in class JobState
-
- isUnvisited(int) - Method in class EncodedIntBuffer
-
- isUnvisited(int) - Method in class EncodedVoxels
-
- isUseLastSeriesIndexOnly() - Method in class NamedChannels
-
- isUseLastSeriesIndexOnly() - Method in class Stacks
-
- isUseMax() - Method in class OverlapRatio
-
- isUseMax() - Method in class OverlapRatioMask
-
- isUseZ() - Method in class KernelApplicationParameters
-
Whether to additionally apply the kernel along the Z dimension, as well as X and Y?
- isUseZ() - Method in class KernelPointCursor
-
Whether to additionally apply the kernel along the Z dimension, as well as X and Y?
- isUseZ() - Method in class RemoveTouchingBorder
-
- isUseZ() - Method in class TraverseOuterContourOnImage
-
- isValidName(String, boolean) - Static method in class RGBChannelNames
-
Whether the channel-name is one of red, green, or blue, or alpha.
- isValidNameSet(Set<String>) - Static method in class RGBChannelNames
-
Do the channel-names correspond exactly to those expected either RGB or RGBA.
- isValidNameSet(Set<String>, boolean) - Static method in class RGBChannelNames
-
Do the channel-names correspond exactly to those expected for one of RGB or RGBA.
- isVaryColors() - Method in class SegmentInstanceWithModel
-
If true the colors change for different objects in the image (using a default color set).
- isVisuallyShortenDecimals() - Method in class ExportFeaturesStyle
-
When true, feature-values are shown as visually compressed as possible, including suppressing
decimal places.
- isVisuallyShortenDecimals() - Method in class FeatureExporterContext
-
When true double values are printed to be as short as possible without losing
precision.
- isVoxelOn(Point3i) - Method in class Mask
-
Does a particular voxel have the on state?
- iterateEntries(CheckedBiConsumer<K, V, E>) - Method in class MapCreate
-
Iterate over each entry in the map, and apply an operation.
- IterateKernelHelper - Class in org.anchoranalysis.image.voxel.iterator.neighbor.kernel
-
- iterateMap(Map<K, V>, CheckedBiConsumer<K, V, E>) - Static method in class FunctionalIterate
-
Iterate through all entries in a
Map.
- iterateOverSlices(Consumer<VoxelBuffer<T>>) - Method in interface SliceBufferIndex
-
Calls sliceConsumer once for each slice with the respective buffer.
- iterateOverSlicesAndOffsets(ProcessVoxelBufferUnary<T>) - Method in interface SliceBufferIndex
-
Calls process for each offset in each slice.
- iterateOverXY(OffsettedScalarTwoDimensionalConsumer<E>) - Method in class Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXY(PointTwoDimensionalConsumer) - Method in class Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXYOffset(CheckedIntConsumer<E>) - Method in class Extent
-
Calls processor once for each x and y-values but only passing an offset.
- iterateOverXYOffset(OffsettedPointTwoDimensionalConsumer) - Method in class Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXYWithShift(Point2i, PointTwoDimensionalConsumer) - Method in class Extent
-
Calls processor once for each x and y-values in the range, with a shift added.
- iterateOverYXOffset(OffsettedPointTwoDimensionalConsumer) - Method in class Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverZ(CheckedIntConsumer<E>) - Method in class Extent
-
Calls processor once for each z-value in the range.
- iterateOverZUntil(IntPredicate) - Method in class Extent
-
Calls processor once for each z-value in the range unless indexPredicate returns
false.
- iterateValues(Histogram.BinConsumer) - Method in class Histogram
-
Calls consumer for every value, increasing from min to max.
- iterateValuesUntil(int, Histogram.BinConsumer) - Method in class Histogram
-
Calls consumer for every value until a limit, increasing from min to limit.
- IterateVoxelsAll - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over
all voxels in one or more
Voxels.
- IterateVoxelsBoundingBox - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of image voxels within a bounding-box.
- IterateVoxelsEqualTo - Class in org.anchoranalysis.image.voxel.iterator
-
- IterateVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
- IterateVoxelsMask - Class in org.anchoranalysis.image.core.mask
-
Utilities for iterating over the subset of voxels corresponding to an
on state in a
Mask.
- IterateVoxelsNeighbors - Class in org.anchoranalysis.image.voxel.iterator.neighbor
-
Utilities for iterating over the neighboring voxels to a given point.
- IterateVoxelsObjectMask - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of voxels corresponding to an
on state in an
ObjectMask.
- IterateVoxelsObjectMaskOptional - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of voxels corresponding to an
on state in an
optional
ObjectMask.
- IterateVoxelsRemaining - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over
remaining voxels in one or more
VoxelBuffers.
- iterator() - Method in class SequenceInteger
-
An iterator for each element in the sequence.
- iterator() - Method in class DoubleList
-
- iterator() - Method in class DoubleSet
-
- iterator() - Method in class IntegerList
-
- iterator() - Method in class IntegerSet
-
- iterator() - Method in class StringList
-
- iterator() - Method in class StringSet
-
- iterator() - Method in class ColorList
-
- iterator() - Method in class NameValueMap
-
- iterator() - Method in class ConcurrentJobMonitor
-
- iterator() - Method in class FeatureList
-
- iterator() - Method in class CombinedName
-
- iterator() - Method in class SimpleName
-
- iterator() - Method in class FeatureNameList
-
- iterator() - Method in class ResultsVectorList
-
- iterator() - Method in class CacheTransferSourceCollection
-
- iterator() - Method in class SharedFeatures
-
- iterator() - Method in class NamedFeatureStore
-
- iterator() - Method in class BoundingBoxesOnPlane
-
- iterator() - Method in class ObjectCollectionWithProperties
-
- iterator() - Method in class Stack
-
- iterator() - Method in class StackNotUniformSized
-
- iterator() - Method in class StackSeries
-
- iterator() - Method in class TimeSequence
-
- iterator() - Method in class ObjectCollection
-
- iterator() - Method in class InputsWithDirectory
-
- iterator() - Method in class EnergySavedInd
-
- iterator() - Method in class EnergySchemeSet
-
- iterator() - Method in class MemoList
-
- iterator() - Method in class UpdatableMarksList
-
- iterator() - Method in class ColoredMarks
-
- iterator() - Method in class MarkCollection
-
- iterator() - Method in class WeightedKernelList
-
- iterator() - Method in class ColoredOverlayCollection
-
- iterator() - Method in class OverlayCollection
-
- iterator() - Method in class OverlayProperties
-
- iterator() - Method in class ImageCounterList
-
- iterator() - Method in class LevelResultCollection
-
- iterator() - Method in class ParsedFilePathBag
-
- iterator() - Method in class SortedSetChannel
-
- iteratorCoupledManifests() - Method in class ManifestCouplingDefinition
-
- iteratorCoupledManifestsFor(Manifest) - Method in class ManifestCouplingDefinition
-
- iteratorExperimentalManifests() - Method in class ManifestCouplingDefinition
-
- iteratorFromRaster() - Method in class NamedChannelsForSeriesConcatenate
-
- ObjectAggregationBase<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
-
Calculates a feature for a set of objects using this stack as a energy-stack, and aggregates.
- ObjectAggregationBase() - Constructor for class ObjectAggregationBase
-
- ObjectAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.mask
-
Writes an object-mask as a mask (i.e.
- ObjectAsMaskGenerator() - Constructor for class ObjectAsMaskGenerator
-
Creates using a default image-resolution.
- ObjectAsMaskGenerator(Optional<Resolution>) - Constructor for class ObjectAsMaskGenerator
-
- ObjectAsPoints - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- ObjectAsPoints() - Constructor for class ObjectAsPoints
-
- ObjectCollection - Class in org.anchoranalysis.image.voxel.object
-
- ObjectCollection() - Constructor for class ObjectCollection
-
Creates with no objects.
- ObjectCollection(Stream<ObjectMask>) - Constructor for class ObjectCollection
-
Creates with elements from a stream.
- ObjectCollectionFactory - Class in org.anchoranalysis.image.voxel.object
-
- ObjectCollectionProvider - Class in org.anchoranalysis.image.bean.provider
-
- ObjectCollectionProvider() - Constructor for class ObjectCollectionProvider
-
- ObjectCollectionProviderFilterBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
-
- ObjectCollectionProviderFilterBase() - Constructor for class ObjectCollectionProviderFilterBase
-
- ObjectCollectionProviderMorphological - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
-
- ObjectCollectionProviderMorphological() - Constructor for class ObjectCollectionProviderMorphological
-
- ObjectCollectionProviderUnary - Class in org.anchoranalysis.image.bean.provider
-
- ObjectCollectionProviderUnary() - Constructor for class ObjectCollectionProviderUnary
-
- ObjectCollectionProviderWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
- ObjectCollectionProviderWithFeature() - Constructor for class ObjectCollectionProviderWithFeature
-
- ObjectCollectionReader - Class in org.anchoranalysis.image.io.object.input
-
- ObjectCollectionWithProperties - Class in org.anchoranalysis.image.core.object.properties
-
- ObjectCollectionWithProperties() - Constructor for class ObjectCollectionWithProperties
-
Create with zero objects.
- ObjectCollectionWithProperties(ObjectMask) - Constructor for class ObjectCollectionWithProperties
-
Create with a single object.
- ObjectCollectionWithProperties(Stream<ObjectWithProperties>) - Constructor for class ObjectCollectionWithProperties
-
Create with a stream of objects with properties.
- ObjectCollectionWithProperties(ObjectCollection) - Constructor for class ObjectCollectionWithProperties
-
Create with a stream of objects, assign empty properties to each.
- ObjectCollectionWithPropertiesFactory - Class in org.anchoranalysis.image.core.object.properties
-
- ObjectCollectionWriter - Class in org.anchoranalysis.image.io.object.output.hdf5
-
- objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in interface VoxelsExtracter
-
Copies an area corresponding to an object-mask to another
Voxels.
- ObjectDrawAttributes - Class in org.anchoranalysis.overlay.writer
-
A means of extracting attributes associated with a particular object (e.g.
- ObjectDrawAttributes(ColorIndex) - Constructor for class ObjectDrawAttributes
-
Creates with a specific color-index and uses the iteration-index as both the ID and color-ID
- ObjectDrawAttributes(ColorIndex, IdentifierGetter<ObjectWithProperties>, IdentifierGetter<ObjectWithProperties>) - Constructor for class ObjectDrawAttributes
-
- ObjectDrawAttributesFactory - Class in org.anchoranalysis.overlay.writer
-
- ObjectFilter - Class in org.anchoranalysis.image.bean.object
-
Base class for filtering an
ObjectCollection to remove objects according to a criteria.
- ObjectFilter() - Constructor for class ObjectFilter
-
- ObjectFilterCombine - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
A filter that combines other filters (in a list)
- ObjectFilterCombine() - Constructor for class ObjectFilterCombine
-
- ObjectFilterPredicate - Class in org.anchoranalysis.plugin.image.bean.object.filter
-
Uses a predicate to make a decision whether to keep objects or not.
- ObjectFilterPredicate() - Constructor for class ObjectFilterPredicate
-
- ObjectFilterRelation - Class in org.anchoranalysis.plugin.image.bean.object.filter
-
An independent object-filter that uses a relation in its predicate.
- ObjectFilterRelation() - Constructor for class ObjectFilterRelation
-
- objectFor(T) - Method in interface AccessObjectMask
-
An object-mask for a given element.
- objectFor(ObjectMask) - Method in class AccessObjectMaskSimple
-
- ObjectFromPointsFactory - Class in org.anchoranalysis.image.core.object
-
- ObjectInputStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize
-
Deserializes using Java's Native serialization framework.
- ObjectInputStreamDeserializer() - Constructor for class ObjectInputStreamDeserializer
-
- ObjectIntersectionRemover - Class in org.anchoranalysis.plugin.image.object
-
- ObjectMask - Class in org.anchoranalysis.image.voxel.object
-
A localized-mask in an image, expressed as a
BoundingBox, with a corresponding mask sized
to match the bounding-box.
- ObjectMask(Voxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
Creates from a
Voxels mask that is cornered at the origin.
- ObjectMask(BoundingBox) - Constructor for class ObjectMask
-
Creates as a bounding-box with all corresponding mask voxels set to off.
- ObjectMask(BoundedVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
- ObjectMask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesInt) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, BinaryVoxels<UnsignedByteBuffer>) - Constructor for class ObjectMask
-
Creates from a
BinaryVoxels and a corresponding bounding-box.
- ObjectMask(BoundedVoxels<UnsignedByteBuffer>, BinaryValuesInt) - Constructor for class ObjectMask
-
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Constructor for class ObjectMask
-
- ObjectMaskMerger - Class in org.anchoranalysis.image.core.merge
-
Merges one or more
ObjectMasks into a single object.
- ObjectMaskStream - Class in org.anchoranalysis.image.voxel.object
-
A custom "stream" like class for various functional-programming operations on
ObjectCollection
- ObjectMaskStream(ObjectCollection) - Constructor for class ObjectMaskStream
-
- ObjectMatcher - Class in org.anchoranalysis.image.bean.object
-
Matches an object with other objects.
- ObjectMatcher() - Constructor for class ObjectMatcher
-
- ObjectOutputStreamGenerator<T extends Serializable> - Class in org.anchoranalysis.io.generator.serialized
-
- ObjectOutputStreamGenerator() - Constructor for class ObjectOutputStreamGenerator
-
- ObjectOutputStreamGenerator(Optional<String>) - Constructor for class ObjectOutputStreamGenerator
-
- ObjectRadiusStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- ObjectRadiusStandardDeviation() - Constructor for class ObjectRadiusStandardDeviation
-
- objects() - Method in class ImageInitialization
-
- objects() - Method in class MultiInput
-
- OBJECTS - Static variable in class OutputterDirectories
-
Where collections of objects are typically placed in a define-experiment output
- Objects - Class in org.anchoranalysis.plugin.annotation.bean.comparer
-
- Objects() - Constructor for class Objects
-
- objects(String) - Static method in class ReferenceFactory
-
- OBJECTS_ROOT - Static variable in class HDF5PathHelper
-
Hardcoded string that identifies in the HDF5 file for where the object-collection is stored
- OBJECTS_ROOT_WITH_SEPERATORS - Static variable in class HDF5PathHelper
-
Adds seperators before and after the OBJECTS_ROOT_PATH
- ObjectsAsGrayscaleGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale
-
Base class for generators that accept a set of objects as input.
- ObjectsAsGrayscaleGenerator(Dimensions) - Constructor for class ObjectsAsGrayscaleGenerator
-
- ObjectsAsRGBGenerator - Class in org.anchoranalysis.image.io.object.output.rgb
-
A base class for generators that draw objects on top of a RGB-Stack.
- ObjectsAsRGBGenerator(DrawObject, ObjectDrawAttributes, Either<Dimensions, DisplayStack>) - Constructor for class ObjectsAsRGBGenerator
-
- ObjectsAsUniqueValueGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale
-
Writes objects as a Raster with unique id values for each object.
- ObjectsAsUniqueValueGenerator(Dimensions) - Constructor for class ObjectsAsUniqueValueGenerator
-
- ObjectScalingMethod - Interface in org.anchoranalysis.image.core.object.scale.method
-
A way to scale a group of
ObjectMasks, scaling each object independently or collectively.
- ObjectScalingMethodFactory - Class in org.anchoranalysis.image.core.object.scale.method
-
- ObjectSerializerPeriodicReporter<T extends Serializable> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- ObjectSerializerPeriodicReporter(String) - Constructor for class ObjectSerializerPeriodicReporter
-
- objectsForThumbnail(T) - Method in class CombineObjectsForFeatures
-
Selects objects from an input that will be used for thumbnail generation
- objectsForThumbnail(FeatureInputSingleObject) - Method in class EachObjectIndependently
-
- objectsForThumbnail(FeatureInputPairObjects) - Method in class PairNeighbors
-
- ObjectsFromConnectedComponentsFactory - Class in org.anchoranalysis.image.voxel.binary.connected
-
Creates a
ObjectCollection from the connected-components of a mask or binary-voxels.
- ObjectsFromConnectedComponentsFactory() - Constructor for class ObjectsFromConnectedComponentsFactory
-
Creates to use a small-neighborhood.
- ObjectsFromConnectedComponentsFactory(boolean) - Constructor for class ObjectsFromConnectedComponentsFactory
-
Creates to use a specified type of neighborhood.
- ObjectsFromConnectedComponentsFactory(int) - Constructor for class ObjectsFromConnectedComponentsFactory
-
Creates to use a minimum number of voxels for each connected component.
- ObjectsFromConnectedComponentsFactory(boolean, int) - Constructor for class ObjectsFromConnectedComponentsFactory
-
Creates to use a specified type of neighborhood, and minimum number of voxels.
- objectsFromOverlays(OverlayCollection) - Static method in class OverlayCollectionObjectFactory
-
Creates objects from whatever Overlays are found in the collection *
- ObjectsMergedAsMaskGenerator - Class in org.anchoranalysis.image.io.object.output.grayscale
-
Writes objects merged together as a mask.
- ObjectsMergedAsMaskGenerator(Dimensions) - Constructor for class ObjectsMergedAsMaskGenerator
-
- ObjectsToCompare - Class in org.anchoranalysis.plugin.annotation.comparison
-
- ObjectsToCompare(ObjectCollection, ObjectCollection) - Constructor for class ObjectsToCompare
-
- objectsToDraw(Dimensions) - Method in class ColoredBaseWithGenerator
-
The objects to draw (without any colors) on the background
- objectsToDraw(Dimensions) - Method in class ColoredObjects
-
- objectsToDraw(Dimensions) - Method in class ColoredMarks
-
- ObjectVertex - Class in org.anchoranalysis.plugin.image.object.merge
-
A vertex in a merge graph representing an object (and and an associated payload)
- ObjectVertex(ObjectMask, double) - Constructor for class ObjectVertex
-
- ObjectVoxelIntersection - Class in org.anchoranalysis.annotation.io.assignment
-
Creates an assignment between intersecting voxels in two objects.
- ObjectVoxelIntersection(ObjectMask, ObjectMask) - Constructor for class ObjectVoxelIntersection
-
Determines a voxel-assignment between two objects.
- ObjectWithBoundingBoxGenerator - Class in org.anchoranalysis.image.io.object.output.mask
-
- ObjectWithBoundingBoxGenerator(Optional<Resolution>) - Constructor for class ObjectWithBoundingBoxGenerator
-
- ObjectWithEllipse - Class in org.anchoranalysis.plugin.points.calculate.ellipse
-
- ObjectWithEllipse(ObjectMask, Ellipse) - Constructor for class ObjectWithEllipse
-
- ObjectWithMaximumFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Finds the object with the maximum feature-value from a collection.
- ObjectWithMaximumFeature() - Constructor for class ObjectWithMaximumFeature
-
- ObjectWithMaximumFeatureFromEachMatchedCollection - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Finds the object with the maximum feature among a group of matches for each object.
- ObjectWithMaximumFeatureFromEachMatchedCollection() - Constructor for class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- ObjectWithProperties - Class in org.anchoranalysis.image.core.object.properties
-
An
ObjectMask with associated key-value properties.
- ObjectWithProperties(BoundingBox) - Constructor for class ObjectWithProperties
-
Creates as a bounding-box with all corresponding mask voxels set to off.
- ObjectWithProperties(ObjectMask) - Constructor for class ObjectWithProperties
-
Creates with an existing
ObjectMask and empty properties.
- ObjectWithProperties(ObjectMask, Map<String, Object>) - Constructor for class ObjectWithProperties
-
- obtain(int, AggregateReceiver<T>, PeriodTriggerBank<T>) - Method in class AggregateTriggerBank
-
- obtain(int, PeriodReceiver<S>) - Method in class PeriodTriggerBank
-
- of(Stream<T>) - Static method in class FunctionalList
-
Creates a list from a stream.
- of(boolean) - Static method in class ObjectScalingMethodFactory
-
Determines which method to use, given circumstances.
- of(boolean, boolean) - Static method in enum OutsideKernelPolicy
-
Multiplexes between all three possible enums.
- of(boolean) - Static method in class NeighborhoodFactory
-
Gets an appropriate neighborhood
- of(ObjectMask...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements from the parameter-list.
- of(ObjectCollection...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections.
- of(Optional<ObjectCollection>...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections, if they exist.
- of(Collection<ObjectMask>...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections.
- of(BinaryVoxels<UnsignedByteBuffer>...) - Static method in class ObjectCollectionFactory
-
Creates a new collection with elements from the parameter-list of
BinaryVoxels
converting the voxels in their entirety to an object-mask at the origin.
- of(CalculationPartResolver<FeatureInputSingleObject>, MorphologicalIterations, int, boolean) - Static method in class CalculateShellObjectMask
-
- of(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateDilation
-
- of(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateErosion
-
- of(FeatureCalculationInput<FeatureInputSingleObject>, boolean) - Static method in class CalculateEllipsoidLeastSquares
-
- offset(int, int) - Method in class Dimensions
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
- offset(Point3i) - Method in class Dimensions
-
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
- offset(int, int) - Method in class Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
- offset(int, int, int) - Method in class Extent
-
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
- offset(ReadableTuple3i) - Method in class Extent
-
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent.
- offset(Point2i) - Method in class Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
- offsetGlobal(int, int) - Method in class ObjectMask
-
Calculates an offset for locating a voxel inside the buffer, with global encoding of
coordinates.
- offsetRelative(int, int) - Method in class ObjectMask
-
Calculates an offset for locating a voxel inside the buffer, with local encoding of
coordinates.
- offsetSlice(Point3i) - Method in class Dimensions
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
- offsetSlice(ReadableTuple3i) - Method in class Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent.
- OffsettedPointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
- OffsettedScalarTwoDimensionalConsumer<E extends Exception> - Interface in org.anchoranalysis.spatial.point.consumer
-
- ofResolved(CalculationPartResolver<FeatureInputSingleObject>, int, boolean) - Static method in class CalculateErosion
-
- OMETiff - Class in org.anchoranalysis.io.bioformats.bean.writer
-
- OMETiff() - Constructor for class OMETiff
-
Default constructor.
- OMEXML - Class in org.anchoranalysis.io.bioformats.bean.writer
-
- OMEXML() - Constructor for class OMEXML
-
Default constructor.
- One - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects one specific channel from a set of stacks
- One() - Constructor for class One
-
- oneOnly(String, String, boolean, boolean) - Static method in class CheckMisconfigured
-
Checks that one of two properties is defined, but not both simultaneously (exclusive OR).
- OneOrThreeChannelsWriter - Class in org.anchoranalysis.image.io.bean.stack.writer
-
A base-class for a raster-writer that writes only one or three channeled images, and a flexible
extension.
- OneOrThreeChannelsWriter() - Constructor for class OneOrThreeChannelsWriter
-
- OneStageGenerator<T> - Class in org.anchoranalysis.io.generator
-
- OneStageGenerator() - Constructor for class OneStageGenerator
-
- ongoingTasksLessThan(int) - Method in class ConcurrentJobMonitor
-
- onInitialization(P) - Method in class InitializableBean
-
Called after initialization.
- onInitialization(NullInitialization) - Method in class NullParametersBean
-
- onInitialization() - Method in class NullParametersBean
-
As there's no parameters we expose a different method.
- onInitialization(DictionaryInitialization) - Method in class DictionaryProviderReference
-
- onInitialization(FeatureInitialization) - Method in class Feature
-
Called after initialization.
- onInitialization(FeatureRelatedInitialization) - Method in class ReferencingFeatureListProvider
-
- onInitialization(ImageInitialization) - Method in class BinarySegmentationReference
-
- onInitialization() - Method in class MarkWithIdentifierFactory
-
- onInitialization(ImageInitialization) - Method in class FromInput
-
- onInitialization(ImageInitialization) - Method in class FromChannel
-
- onInitialization(ImageInitialization) - Method in class Reference
-
- onInitialization(ImageInitialization) - Method in class FromStackChannel
-
- onInitialization(ImageInitialization) - Method in class ReferenceOrElse
-
- onInitialization(ImageInitialization) - Method in class FromInput
-
- onInitialization(FeatureRelatedInitialization) - Method in class PermuteFeature
-
- onInitialization(MarksInitialization) - Method in class FeatureValueCheckMark
-
- onInitialization(MarksInitialization) - Method in class MarkProposerReference
-
- onInitialization(MarksInitialization) - Method in class MarkMergeProposerReference
-
- onInitialization(MarksInitialization) - Method in class MarkSplitProposerReference
-
- onInitialization(MarksInitialization) - Method in class KernelMerge
-
- onInitialization(PointsInitialization) - Method in class Reference
-
- OnlyIf - Class in org.anchoranalysis.experiment.bean.log
-
Logs messages to a particular location ONLY if certain conditions are fulfilled.
- OnlyIf() - Constructor for class OnlyIf
-
- OnnxModel - Class in org.anchoranalysis.plugin.onnx.model
-
A model that can be used for inference using the
ONNX
Runtime's Java API.
- OnnxModel(OrtSession) - Constructor for class OnnxModel
-
- open() - Method in interface Progress
-
- open() - Method in class ProgressConsole
-
- open() - Method in class ProgressIgnore
-
- open() - Method in class ProgressIncrement
-
- open(Logger) - Method in interface OpenedImageFile
-
Open the first series when we don't have a specific-type.
- open(int, Logger) - Method in interface OpenedImageFile
-
Open when we don't have a specific-type.
- open(int, Progress, Logger) - Method in interface OpenedImageFile
-
- open(Path) - Static method in class CSVReaderByLine
-
Default reader, using comma and first-line headers
- open(Path, String, boolean) - Static method in class CSVReaderByLine
-
Default reader, using comma and first-line headers
- open(Path, String, boolean, boolean) - Static method in class CSVReaderByLine
-
Default reader, using comma and first-line headers
- open(int, Progress, Logger) - Method in class OpenedMultiFile
-
- openCheckType(int, Progress, VoxelDataType, Logger) - Method in interface OpenedImageFile
-
Opens a time-series, and checks that it is a particular type.
- OpenCVModel - Class in org.anchoranalysis.plugin.opencv.segment
-
- OpenCVModel(Net) - Constructor for class OpenCVModel
-
- OpenCVReader - Class in org.anchoranalysis.plugin.opencv.bean.stack
-
Reads a stack from the file-system using OpenCV.
- OpenCVReader() - Constructor for class OpenCVReader
-
- OpenCVWriter - Class in org.anchoranalysis.plugin.opencv.bean.stack
-
Writes a stack to the file-system using OpenCV and a specified extension.
- OpenCVWriter() - Constructor for class OpenCVWriter
-
- OpenedCSVFile() - Constructor for class CSVReader.OpenedCSVFile
-
- OpenedImageFile - Interface in org.anchoranalysis.image.io.stack.input
-
An image file that has been opened for reading containing one or more series of image-
Stacks.
- OpenedMultiFile - Class in org.anchoranalysis.plugin.io.multifile
-
A
OpenedImageFile where the image is formed from more than one file on the file-system.
- OpenedMultiFile(StackReader, ParsedFilePathBag) - Constructor for class OpenedMultiFile
-
- openFile(Path, StackReader, Logger) - Method in class ImageMetadataReader
-
Opens a file containing one or more images but does not read an image.
- openFile(Path) - Method in class StackReader
-
Opens a file containing one or more images.
- openFile(Path, CalculateOrientationChange) - Method in class StackReaderOrientationCorrection
-
Opens a file containing one or more images but does not read an image.
- openFile(Path) - Method in class BioformatsReader
-
- openFile(Path, CalculateOrientationChange) - Method in class BioformatsReader
-
- openFile(Path, StackReader, Logger) - Method in class AlwaysReject
-
- openFile(Path, StackReader, Logger) - Method in class FromStackReader
-
- openFile(Path, StackReader, Logger) - Method in class InferFromHeader
-
- openFile(Path) - Method in class BranchExtension
-
- openFile(Path) - Method in class FlattenAsChannel
-
- openFile(Path) - Method in class ImposeResolution
-
- openFile(Path) - Method in class MultiFileReader
-
- openFile(Path) - Method in class ReadVoxelExtentXml
-
- openFile(Path) - Method in class RejectIfConditionXYResolution
-
- openFile(Path) - Method in class RotateImageToMatchEXIFOrientation
-
- openFile(Path, CalculateOrientationChange) - Method in class RotateImageToMatchEXIFOrientation
-
- openFile(Path) - Method in class OpenCVReader
-
- openMarksFromFilePath(Path) - Static method in class TestLoaderMarks
-
- openMarksFromTestPath(String) - Method in class TestLoaderMarks
-
- openMask(StackReader, Path, BinaryValuesInt, Logger) - Static method in class MaskReader
-
Utility functions for opening a single-channeled stack as a
Mask.
- openXmlAbsoluteFilePath(String) - Static method in class TestLoader
-
Opens a XML document - with an absolute path on the filesystem.
- openXmlAbsoluteFilePath(Path) - Static method in class TestLoader
-
Opens a XML document - with an absolute path on the filesystem.
- openXmlFromTestPath(String) - Method in class TestLoader
-
Opens a XML document - with a path relative to the test root.
- OperationFailedException - Exception in org.anchoranalysis.core.exception
-
Generic checked exception that can be thrown when a particular operation fails.
- OperationFailedException(String) - Constructor for exception OperationFailedException
-
Creates with only a message.
- OperationFailedException(Throwable) - Constructor for exception OperationFailedException
-
Creates with only a cause.
- OperationFailedException(String, Throwable) - Constructor for exception OperationFailedException
-
Creates with both a message and cause.
- OperationFailedRuntimeException - Exception in org.anchoranalysis.core.exception
-
Generic runtime exception that can be thrown when a particular operation fails.
- OperationFailedRuntimeException(String) - Constructor for exception OperationFailedRuntimeException
-
Creates with only a message.
- OperationFailedRuntimeException(Exception) - Constructor for exception OperationFailedRuntimeException
-
Creates with only a cause.
- OperationMap<T> - Class in org.anchoranalysis.mpp.io.input
-
Stores objects as operations
- OperationMap() - Constructor for class OperationMap
-
- OptimizationContext - Class in org.anchoranalysis.mpp.segment.optimization
-
- OptimizationContext(String, EnergySchemeWithSharedFeatures, DualStack, TriggerTerminationCondition, InputOutputContext, RandomNumberGenerator, MarkWithIdentifierFactory) - Constructor for class OptimizationContext
-
- OptimizationScheme<S,U,V> - Class in org.anchoranalysis.mpp.segment.bean.optimization
-
An optimization-scheme that uses kernels to make changes to state.
- OptimizationScheme() - Constructor for class OptimizationScheme
-
- OptimizationStep<S,T,V> - Class in org.anchoranalysis.mpp.segment.optimization.step
-
- OptimizationStep() - Constructor for class OptimizationStep
-
- OptimizationStepLogReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- OptimizationStepLogReporter() - Constructor for class OptimizationStepLogReporter
-
- OptimizationTerminatedEarlyException - Exception in org.anchoranalysis.mpp.segment.optimization
-
- OptimizationTerminatedEarlyException(String, Throwable) - Constructor for exception OptimizationTerminatedEarlyException
-
- OptionalBean - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a field of a class can be set to null (omitted), otherwise by default a bean must
always have a non-null value.
- OptionalFactory - Class in org.anchoranalysis.core.functional
-
Utility functions to create
Optional from flags.
- OptionalNameValue<V> - Class in org.anchoranalysis.io.generator.combined
-
A simple container expressing a value and an associationed optional name.
- OptionalNameValue(Optional<String>, V) - Constructor for class OptionalNameValue
-
- OptionalPointProposer - Interface in org.anchoranalysis.mpp.proposer
-
- OptionalProviderFactory - Class in org.anchoranalysis.bean
-
- OptionalUtilities - Class in org.anchoranalysis.core.functional
-
Additional utility functions for
Optional and exceptions.
- or(StackWriteAttributes) - Method in class StackWriteAttributes
-
- Or - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation or voxelwise on both masks, modifying {mask} with the
result.
- Or() - Constructor for class Or
-
- Or - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
Applies multiples filter with logical OR i.e.
- Or() - Constructor for class Or
-
- order(String) - Method in interface OrderProvider
-
- OrderedFeatureList<T extends FeatureInput> - Interface in org.anchoranalysis.mpp.feature.addcriteria
-
- OrderedList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- OrderedList() - Constructor for class OrderedList
-
- orderedListOfFeatures() - Method in class AddCriteriaEnergyPair
-
- orderedListOfFeatures() - Method in class AddCriteriaNever
-
- orderedListOfFeatures() - Method in class AddCriteriaOr
-
- orderedListOfFeatures() - Method in class ArbitraryPointCommon
-
- orderedListOfFeatures() - Method in class BoundingBoxIntersection
-
- orderedListOfFeatures() - Method in interface OrderedFeatureList
-
- orderedListOfFeatures() - Method in class AddCriteriaFeatureRelationThreshold
-
- OrderedRadius - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
-
- OrderedRadius() - Constructor for class OrderedRadius
-
- OrderProvider - Interface in org.anchoranalysis.io.manifest.sequencetype
-
- orElseGet(Optional<T>, CheckedSupplier<T, E>) - Static method in class OptionalUtilities
-
- orElseGetFlat(Optional<T>, CheckedSupplier<Optional<T>, E>...) - Static method in class OptionalUtilities
-
- orFlat(Iterable<Optional<T>>) - Static method in class OptionalUtilities
-
The first optional if it's present, or the second, or the third etc.
- orFlat(Stream<Optional<T>>) - Static method in class OptionalUtilities
-
The first optional if it's present, or the second, or the third etc.
- orFlat(Optional<T>...) - Static method in class OptionalUtilities
-
- orFlatSupplier(Iterable<CheckedSupplier<Optional<T>, E>>) - Static method in class OptionalUtilities
-
The first optional if it's present, or the second, or the third etc.
- orFlatSupplier(CheckedSupplier<Optional<T>, E>...) - Static method in class OptionalUtilities
-
- org.anchoranalysis.annotation - package org.anchoranalysis.annotation
-
Ground truth for an image in diverse forms.
- org.anchoranalysis.annotation.image - package org.anchoranalysis.annotation.image
-
Annotations that apply to an image as a whole.
- org.anchoranalysis.annotation.io - package org.anchoranalysis.annotation.io
-
Reading and writing annotations to the filesystem.
- org.anchoranalysis.annotation.io.assignment - package org.anchoranalysis.annotation.io.assignment
-
A pairing of objects from two collections (bipartite matching).
- org.anchoranalysis.annotation.io.assignment.generator - package org.anchoranalysis.annotation.io.assignment.generator
-
Generates output images to illustrate a
Assignment between annotations.
- org.anchoranalysis.annotation.io.bean - package org.anchoranalysis.annotation.io.bean
-
Beans related to reading / writing / specifying annotations.
- org.anchoranalysis.annotation.io.bean.comparer - package org.anchoranalysis.annotation.io.bean.comparer
-
What to compare an annotation (ground truth) against?
- org.anchoranalysis.annotation.io.comparer - package org.anchoranalysis.annotation.io.comparer
-
Non-bean classes involving comparing results and annotations.
- org.anchoranalysis.annotation.io.image - package org.anchoranalysis.annotation.io.image
-
Reading and writing whole-image label annotations.
- org.anchoranalysis.annotation.io.image.findable - package org.anchoranalysis.annotation.io.image.findable
-
The outcome of searching for annotations or images on the file-system.
- org.anchoranalysis.annotation.io.mark - package org.anchoranalysis.annotation.io.mark
-
Reading and writing
Mark-related annotations from/to the
file-system.
- org.anchoranalysis.annotation.mark - package org.anchoranalysis.annotation.mark
-
Annotations that use one or more marks to describe entities in an image.
- org.anchoranalysis.bean - package org.anchoranalysis.bean
-
- org.anchoranalysis.bean.annotation - package org.anchoranalysis.bean.annotation
-
- org.anchoranalysis.bean.define - package org.anchoranalysis.bean.define
-
- org.anchoranalysis.bean.define.adder - package org.anchoranalysis.bean.define.adder
-
- org.anchoranalysis.bean.exception - package org.anchoranalysis.bean.exception
-
Exceptions that can occur executing generic operations on
Anchor Beans.
- org.anchoranalysis.bean.initializable - package org.anchoranalysis.bean.initializable
-
Initializing beans with particular parameters, including recursively.
- org.anchoranalysis.bean.initializable.parameters - package org.anchoranalysis.bean.initializable.parameters
-
Some parameterization used when initializing beans.
- org.anchoranalysis.bean.initializable.property - package org.anchoranalysis.bean.initializable.property
-
Initializating a bean with parameters.
- org.anchoranalysis.bean.permute - package org.anchoranalysis.bean.permute
-
Applying permutations to a bean's fields.
- org.anchoranalysis.bean.permute.assign - package org.anchoranalysis.bean.permute.assign
-
Imposes a permutation value on one or more properties of a bean.
- org.anchoranalysis.bean.permute.property - package org.anchoranalysis.bean.permute.property
-
Applying permutations to the properties of a bean.
- org.anchoranalysis.bean.primitive - package org.anchoranalysis.bean.primitive
-
Beans that implement collections of primitive element types, as well as
String.
- org.anchoranalysis.bean.shared - package org.anchoranalysis.bean.shared
-
Utility beans which have a generally broader use than a specific module.
- org.anchoranalysis.bean.shared.color - package org.anchoranalysis.bean.shared.color
-
Beans that specify colors.
- org.anchoranalysis.bean.shared.color.scheme - package org.anchoranalysis.bean.shared.color.scheme
-
Beans that create lists or indices of colors according to particular schemes.
- org.anchoranalysis.bean.shared.dictionary - package org.anchoranalysis.bean.shared.dictionary
-
Setting, referencing and initializing key-value parameters.
- org.anchoranalysis.bean.shared.path - package org.anchoranalysis.bean.shared.path
-
Defines a root path directory on the filesystem whre files are read / written.
- org.anchoranalysis.bean.shared.random - package org.anchoranalysis.bean.shared.random
-
Specifies a particular type of random-number generator.
- org.anchoranalysis.bean.shared.regex - package org.anchoranalysis.bean.shared.regex
-
Specifies regular-expressions.
- org.anchoranalysis.bean.shared.relation - package org.anchoranalysis.bean.shared.relation
-
Specifies a binary relation of some kind between scalars.
- org.anchoranalysis.bean.shared.relation.threshold - package org.anchoranalysis.bean.shared.relation.threshold
-
Specifies a unary relation to a threshold value.
- org.anchoranalysis.bean.xml - package org.anchoranalysis.bean.xml
-
Reading Beans from XML files.
- org.anchoranalysis.bean.xml.creator - package org.anchoranalysis.bean.xml.creator
-
Creates beans from XML.
- org.anchoranalysis.bean.xml.exception - package org.anchoranalysis.bean.xml.exception
-
Exceptions that can thrown when loading beans from XML.
- org.anchoranalysis.bean.xml.factory - package org.anchoranalysis.bean.xml.factory
-
Custom factories for loading beans in custom ways from XML.
- org.anchoranalysis.bean.xml.factory.primitive - package org.anchoranalysis.bean.xml.factory.primitive
-
Factories to create beans in org.anchoranalysis.bean.primitive.
- org.anchoranalysis.browser.launcher - package org.anchoranalysis.browser.launcher
-
Launching the anchor GUI interactive application from command-line.
- org.anchoranalysis.core.cache - package org.anchoranalysis.core.cache
-
Caching (memozing) calls to a method so an operation does not need to be repeated.
- org.anchoranalysis.core.color - package org.anchoranalysis.core.color
-
Specifying particular colors and groups of colors.
- org.anchoranalysis.core.exception - package org.anchoranalysis.core.exception
-
Very general exceptions and base classes for exceptions with wide applicability.
- org.anchoranalysis.core.exception.combinable - package org.anchoranalysis.core.exception.combinable
-
Nested exceptions of similar type that can be combined together in a summary.
- org.anchoranalysis.core.exception.friendly - package org.anchoranalysis.core.exception.friendly
-
Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly
error descriptions.
- org.anchoranalysis.core.format - package org.anchoranalysis.core.format
-
File formats and associated extensions.
- org.anchoranalysis.core.functional - package org.anchoranalysis.core.functional
-
Utilities and interfaces for applying functional-programming.
- org.anchoranalysis.core.functional.checked - package org.anchoranalysis.core.functional.checked
-
Versions of many functional-interfaces in java.util.function that throw
checked-exceptions.
- org.anchoranalysis.core.functional.unchecked - package org.anchoranalysis.core.functional.unchecked
-
Adds additional functional-interfaces, that are unavailable in java.util.function, and do
not throw checked exceptions.
- org.anchoranalysis.core.graph - package org.anchoranalysis.core.graph
-
Data-structures for directed and undirected graphs, with or without an edge payload.
- org.anchoranalysis.core.identifier.getter - package org.anchoranalysis.core.identifier.getter
-
Data structures for adding a unique name (a String or integer identifier) to other entities.
- org.anchoranalysis.core.identifier.name - package org.anchoranalysis.core.identifier.name
-
Data structures for name (String) and value associations.
- org.anchoranalysis.core.identifier.provider - package org.anchoranalysis.core.identifier.provider
-
A collection of named-elements, a
NamedProvider and related operations.
- org.anchoranalysis.core.identifier.provider.store - package org.anchoranalysis.core.identifier.provider.store
-
Data structures like
NamedProvider with
supporting for adding new elements.
- org.anchoranalysis.core.index - package org.anchoranalysis.core.index
-
Classes to support getting / setting / specifying unique-integers (indices) for elements.
- org.anchoranalysis.core.index.range - package org.anchoranalysis.core.index.range
-
A range of indices from minimum to maximum.
- org.anchoranalysis.core.log - package org.anchoranalysis.core.log
-
Interfaces to log messages, both information and error messages.
- org.anchoranalysis.core.log.error - package org.anchoranalysis.core.log.error
-
Mechanism for reporting errors (exceptions/throwables) to the user.
- org.anchoranalysis.core.progress - package org.anchoranalysis.core.progress
-
Classes to allow for tracking the progress of a task that can be broken into smaller units, for
reporting to the user.
- org.anchoranalysis.core.random - package org.anchoranalysis.core.random
-
Generating random numbers.
- org.anchoranalysis.core.serialize - package org.anchoranalysis.core.serialize
-
Utilities for serializing and deserializing objects.
- org.anchoranalysis.core.system - package org.anchoranalysis.core.system
-
Utilities for interacting with the operating system or computer system generally
- org.anchoranalysis.core.system.path - package org.anchoranalysis.core.system.path
-
Utilities for converting/manipulating file-paths.
- org.anchoranalysis.core.time - package org.anchoranalysis.core.time
-
Recording the execution-time of operations for profiling.
- org.anchoranalysis.core.value - package org.anchoranalysis.core.value
-
Encapsulating values or sets of named-values.
- org.anchoranalysis.experiment - package org.anchoranalysis.experiment
-
Classes related to executing an experiment by calling jobs on inputs.
- org.anchoranalysis.experiment.arguments - package org.anchoranalysis.experiment.arguments
-
Arguments that can further specify an experiment in addition to its bean specification.
- org.anchoranalysis.experiment.bean - package org.anchoranalysis.experiment.bean
-
Beans related to executing an experiment by calling jobs on inputs.
- org.anchoranalysis.experiment.bean.identifier - package org.anchoranalysis.experiment.bean.identifier
-
Assigning unique names to experiments.
- org.anchoranalysis.experiment.bean.io - package org.anchoranalysis.experiment.bean.io
-
Generic experiments that handle input and output in structured ways.
- org.anchoranalysis.experiment.bean.log - package org.anchoranalysis.experiment.bean.log
-
Different approaches to where messages on the progress/status of an experiment are logged to.
- org.anchoranalysis.experiment.bean.processor - package org.anchoranalysis.experiment.bean.processor
-
How a task is executed on multiple inputs.
- org.anchoranalysis.experiment.bean.require - package org.anchoranalysis.experiment.bean.require
-
A test whether certain conditions on arguments to experiments are fulfilled.
- org.anchoranalysis.experiment.bean.task - package org.anchoranalysis.experiment.bean.task
-
Defines a
task,
which is a set of operations run on an input, that may or may not generate an output.
- org.anchoranalysis.experiment.io - package org.anchoranalysis.experiment.io
-
Interfaces for replacing attributes of an experiment: input, output, task etc.
- org.anchoranalysis.experiment.log - package org.anchoranalysis.experiment.log
-
Helpful classes for logging.
- org.anchoranalysis.experiment.task - package org.anchoranalysis.experiment.task
-
Non-bean classes related to a
Task.
- org.anchoranalysis.experiment.task.processor - package org.anchoranalysis.experiment.task.processor
-
- org.anchoranalysis.experiment.time - package org.anchoranalysis.experiment.time
-
How long particular operations take to execute.
- org.anchoranalysis.feature.bean - package org.anchoranalysis.feature.bean
-
Beans pertaining to feature-calculation.
- org.anchoranalysis.feature.bean.list - package org.anchoranalysis.feature.bean.list
-
A feature-list (custom list type for features) and associated providers.
- org.anchoranalysis.feature.bean.operator - package org.anchoranalysis.feature.bean.operator
-
Features that are sufficiently generic to work on any input-type.
- org.anchoranalysis.feature.bean.provider - package org.anchoranalysis.feature.bean.provider
-
Provider of a single feature.
- org.anchoranalysis.feature.bean.results - package org.anchoranalysis.feature.bean.results
-
- org.anchoranalysis.feature.calculate - package org.anchoranalysis.feature.calculate
-
Sub-feature units of calculation that can be cached.
- org.anchoranalysis.feature.calculate.bound - package org.anchoranalysis.feature.calculate.bound
-
- org.anchoranalysis.feature.calculate.cache - package org.anchoranalysis.feature.calculate.cache
-
Classes to cache feature-results or parts of feature-results that occur repeatedly among features
or across calculations of the same feature.
- org.anchoranalysis.feature.calculate.cache.part - package org.anchoranalysis.feature.calculate.cache.part
-
Equivalent classes to org.anchoranalysis.feature.calculate.part after having been
resolved against a cache.
- org.anchoranalysis.feature.calculate.part - package org.anchoranalysis.feature.calculate.part
-
- org.anchoranalysis.feature.energy - package org.anchoranalysis.feature.energy
-
A particular stack used in feature-calculations called a
EnergyStack together with related classes.
- org.anchoranalysis.feature.initialization - package org.anchoranalysis.feature.initialization
-
Initialization parameters used for beans in org.anchoranalysis.feature.bean.
- org.anchoranalysis.feature.input - package org.anchoranalysis.feature.input
-
Base classes providing inputs to feature calculations.
- org.anchoranalysis.feature.io.csv - package org.anchoranalysis.feature.io.csv
-
Writing feature calculation-results in CSV format.
- org.anchoranalysis.feature.io.name - package org.anchoranalysis.feature.io.name
-
Naming items in a weay that breaks down into multiple elements.
- org.anchoranalysis.feature.io.results - package org.anchoranalysis.feature.io.results
-
Writes feature-calculation results in different formats, also grouped results.
- org.anchoranalysis.feature.io.results.calculation - package org.anchoranalysis.feature.io.results.calculation
-
- org.anchoranalysis.feature.io.results.group - package org.anchoranalysis.feature.io.results.group
-
- org.anchoranalysis.feature.name - package org.anchoranalysis.feature.name
-
Data objects for the names of features.
- org.anchoranalysis.feature.results - package org.anchoranalysis.feature.results
-
Results from one or more feature calculations.
- org.anchoranalysis.feature.session - package org.anchoranalysis.feature.session
-
A defined context in which one or more features are provided inputs and produce results.
- org.anchoranalysis.feature.session.cache - package org.anchoranalysis.feature.session.cache
-
- org.anchoranalysis.feature.session.cache.finder - package org.anchoranalysis.feature.session.cache.finder
-
Strategies to determine which child-cache (among hierarchy) to employ for a particular feature
calculation.
- org.anchoranalysis.feature.session.calculator - package org.anchoranalysis.feature.session.calculator
-
Base classes for methods to calculate results from features.
- org.anchoranalysis.feature.session.replace - package org.anchoranalysis.feature.session.replace
-
Strategies on whether to reuse or invalidate a feature-input's cache.
- org.anchoranalysis.feature.shared - package org.anchoranalysis.feature.shared
-
Features shared for referencing among calculations.
- org.anchoranalysis.feature.store - package org.anchoranalysis.feature.store
-
- org.anchoranalysis.image.bean - package org.anchoranalysis.image.bean
-
Core (bean) classes for image processing.
- org.anchoranalysis.image.bean.channel.converter - package org.anchoranalysis.image.bean.channel.converter
-
Base classes for comparing a channel to another type.
- org.anchoranalysis.image.bean.interpolator - package org.anchoranalysis.image.bean.interpolator
-
Beans for specifying image interpolators.
- org.anchoranalysis.image.bean.nonbean.error - package org.anchoranalysis.image.bean.nonbean.error
-
Specific exception types that can be thrown in this module.
- org.anchoranalysis.image.bean.nonbean.init - package org.anchoranalysis.image.bean.nonbean.init
-
Initialization of image-related beans.
- org.anchoranalysis.image.bean.nonbean.segment - package org.anchoranalysis.image.bean.nonbean.segment
-
Non-bean classes relating to image-segmentation.
- org.anchoranalysis.image.bean.nonbean.spatial.arrange - package org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
Non-beans to specify how to form a single-image by spatially combining other images.
- org.anchoranalysis.image.bean.object - package org.anchoranalysis.image.bean.object
-
Beans pertaining to
ObjectMask and their
collections.
- org.anchoranalysis.image.bean.provider - package org.anchoranalysis.image.bean.provider
-
Base classes for providers of different core data entities related to images.
- org.anchoranalysis.image.bean.provider.stack - package org.anchoranalysis.image.bean.provider.stack
-
- org.anchoranalysis.image.bean.segment - package org.anchoranalysis.image.bean.segment
-
Base classes to perform image segmentation, transforming an image into another meaningful entity
or entities.
- org.anchoranalysis.image.bean.segment.binary - package org.anchoranalysis.image.bean.segment.binary
-
Base classes to perform binary-segmentation.
- org.anchoranalysis.image.bean.segment.object - package org.anchoranalysis.image.bean.segment.object
-
Base classes to segment a channel into objects.
- org.anchoranalysis.image.bean.spatial - package org.anchoranalysis.image.bean.spatial
-
Beans to define entities or operate that consider Euclidian space.
- org.anchoranalysis.image.bean.spatial.arrange - package org.anchoranalysis.image.bean.spatial.arrange
-
Beans to specify how to form a single-image by spatially combining other images.
- org.anchoranalysis.image.bean.spatial.direction - package org.anchoranalysis.image.bean.spatial.direction
-
Beans to specify a direction.
- org.anchoranalysis.image.bean.threshold - package org.anchoranalysis.image.bean.threshold
-
Base classes for thresholding and calculating levels for thresholding.
- org.anchoranalysis.image.bean.threshold.relation - package org.anchoranalysis.image.bean.threshold.relation
-
Reusable relations to a threshold.
- org.anchoranalysis.image.bean.unitvalue.distance - package org.anchoranalysis.image.bean.unitvalue.distance
-
Converting quantities of distance between units.
- org.anchoranalysis.image.bean.unitvalue.extent - package org.anchoranalysis.image.bean.unitvalue.extent
-
Converting quantities of extent (area or volume) between units.
- org.anchoranalysis.image.bean.unitvalue.extent.area - package org.anchoranalysis.image.bean.unitvalue.extent.area
-
Converting quantities of area between units.
- org.anchoranalysis.image.bean.unitvalue.extent.volume - package org.anchoranalysis.image.bean.unitvalue.extent.volume
-
Converting quantities of volume between units.
- org.anchoranalysis.image.core.bufferedimage - package org.anchoranalysis.image.core.bufferedimage
-
- org.anchoranalysis.image.core.channel - package org.anchoranalysis.image.core.channel
-
The
Channel core data-class and related operations
and converters.
- org.anchoranalysis.image.core.channel.convert - package org.anchoranalysis.image.core.channel.convert
-
Converts a channel to other data-types.
- org.anchoranalysis.image.core.channel.convert.attached - package org.anchoranalysis.image.core.channel.convert.attached
-
Converts a channel to another data-type based upon another object to which it is attached.
- org.anchoranalysis.image.core.channel.convert.attached.channel - package org.anchoranalysis.image.core.channel.convert.attached.channel
-
Converts a channel to another data-type based upon a
Channel to which it is
attached.
- org.anchoranalysis.image.core.channel.convert.attached.histogram - package org.anchoranalysis.image.core.channel.convert.attached.histogram
-
Converts a channel to another data-type based upon a
Histogram to which it is
attached.
- org.anchoranalysis.image.core.channel.factory - package org.anchoranalysis.image.core.channel.factory
-
Factory classes for creating
Channel for various
voxel data-types.
- org.anchoranalysis.image.core.contour - package org.anchoranalysis.image.core.contour
-
Finds outline voxels, the pixels on the contour/edge of the object.
- org.anchoranalysis.image.core.dimensions - package org.anchoranalysis.image.core.dimensions
-
Classes to describe the size of images or components of images both in voxels and physically.
- org.anchoranalysis.image.core.dimensions.size.suggestion - package org.anchoranalysis.image.core.dimensions.size.suggestion
-
Suggestions on a size for an image.
- org.anchoranalysis.image.core.mask - package org.anchoranalysis.image.core.mask
-
An image with only two permissible states.
- org.anchoranalysis.image.core.mask.combine - package org.anchoranalysis.image.core.mask.combine
-
Binary operations involving voxelwise combination of
Mask.
- org.anchoranalysis.image.core.merge - package org.anchoranalysis.image.core.merge
-
Merges two or more entities.
- org.anchoranalysis.image.core.object - package org.anchoranalysis.image.core.object
-
The key data entity org.anchoranalysis.image.voxel.object and related-classes and
operations.
- org.anchoranalysis.image.core.object.label - package org.anchoranalysis.image.core.object.label
-
Labelling elements (object-masks or similar) with unique successive integers in a channel.
- org.anchoranalysis.image.core.object.properties - package org.anchoranalysis.image.core.object.properties
-
- org.anchoranalysis.image.core.object.scale - package org.anchoranalysis.image.core.object.scale
-
Scaling object-collections, or lists of elements with object-representations.
- org.anchoranalysis.image.core.object.scale.method - package org.anchoranalysis.image.core.object.scale.method
-
Scaling elements with an associated
ObjectMask
either collectively or independently.
- org.anchoranalysis.image.core.points - package org.anchoranalysis.image.core.points
-
Operations that extract points from image data entities or vice versa.
- org.anchoranalysis.image.core.stack - package org.anchoranalysis.image.core.stack
-
Defines the key data object,
Stack, and related
classes.
- org.anchoranalysis.image.core.stack.named - package org.anchoranalysis.image.core.stack.named
-
A collection of
Stacks, each with a unique identifier
as a name.
- org.anchoranalysis.image.feature.bean - package org.anchoranalysis.image.feature.bean
-
Beans pertaining to feature definition and calculation.
- org.anchoranalysis.image.feature.bean.evaluator - package org.anchoranalysis.image.feature.bean.evaluator
-
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
- org.anchoranalysis.image.feature.bean.histogram - package org.anchoranalysis.image.feature.bean.histogram
-
- org.anchoranalysis.image.feature.bean.object.collection - package org.anchoranalysis.image.feature.bean.object.collection
-
- org.anchoranalysis.image.feature.bean.object.pair - package org.anchoranalysis.image.feature.bean.object.pair
-
- org.anchoranalysis.image.feature.bean.object.single - package org.anchoranalysis.image.feature.bean.object.single
-
- org.anchoranalysis.image.feature.bean.physical - package org.anchoranalysis.image.feature.bean.physical
-
Features that convert to/from physical spatial units (e.g.
- org.anchoranalysis.image.feature.calculation - package org.anchoranalysis.image.feature.calculation
-
- org.anchoranalysis.image.feature.calculator - package org.anchoranalysis.image.feature.calculator
-
Implementations of
FeatureCalculatorMulti
related to images, especially to create tables of feature-calculations.
- org.anchoranalysis.image.feature.calculator.merged - package org.anchoranalysis.image.feature.calculator.merged
-
A particular implementation of
FeatureCalculatorMulti for feature-calculations based
upon pairs of image-objects.
- org.anchoranalysis.image.feature.input - package org.anchoranalysis.image.feature.input
-
- org.anchoranalysis.image.io - package org.anchoranalysis.image.io
-
Reading and writing of image-related data objects to and from the filesystem.
- org.anchoranalysis.image.io.bean.channel - package org.anchoranalysis.image.io.bean.channel
-
Beans pertaining to reading
Channels as input.
- org.anchoranalysis.image.io.bean.object.draw - package org.anchoranalysis.image.io.bean.object.draw
-
How to represent an object-mask in a raster that is being drawn.
- org.anchoranalysis.image.io.bean.object.feature - package org.anchoranalysis.image.io.bean.object.feature
-
- org.anchoranalysis.image.io.bean.stack.combine - package org.anchoranalysis.image.io.bean.stack.combine
-
Beans to combine multiple stacks into a single stack before outputting.
- org.anchoranalysis.image.io.bean.stack.metadata.reader - package org.anchoranalysis.image.io.bean.stack.metadata.reader
-
- org.anchoranalysis.image.io.bean.stack.reader - package org.anchoranalysis.image.io.bean.stack.reader
-
Bean classes for reading raster-files from the filesystem.
- org.anchoranalysis.image.io.bean.stack.writer - package org.anchoranalysis.image.io.bean.stack.writer
-
Bean classes for writing raster-files to the filesystem.
- org.anchoranalysis.image.io.channel.input - package org.anchoranalysis.image.io.channel.input
-
Non-bean classes for reading a
Channel from the
filesystem.
- org.anchoranalysis.image.io.channel.input.series - package org.anchoranalysis.image.io.channel.input.series
-
Non-bean classes for reading a
series of Channels from the filesystem.
- org.anchoranalysis.image.io.channel.output - package org.anchoranalysis.image.io.channel.output
-
Non-bean classes for writing a
Channel to the
filesystem.
- org.anchoranalysis.image.io.histogram.input - package org.anchoranalysis.image.io.histogram.input
-
Non-bean classes for reading a
Histogram from the
filesystem.
- org.anchoranalysis.image.io.histogram.output - package org.anchoranalysis.image.io.histogram.output
-
Non-bean classes for writing a
Histogram to the
filesystem.
- org.anchoranalysis.image.io.object - package org.anchoranalysis.image.io.object
-
Non-bean classes for reading / writing an
ObjectCollection from and to the filesystem.
- org.anchoranalysis.image.io.object.input - package org.anchoranalysis.image.io.object.input
-
- org.anchoranalysis.image.io.object.output.grayscale - package org.anchoranalysis.image.io.object.output.grayscale
-
- org.anchoranalysis.image.io.object.output.hdf5 - package org.anchoranalysis.image.io.object.output.hdf5
-
- org.anchoranalysis.image.io.object.output.mask - package org.anchoranalysis.image.io.object.output.mask
-
Writing an
ObjectCollection to the filesystem as
multiple binary singled-channeled images.
- org.anchoranalysis.image.io.object.output.rgb - package org.anchoranalysis.image.io.object.output.rgb
-
- org.anchoranalysis.image.io.stack - package org.anchoranalysis.image.io.stack
-
Non-bean classes for reading / writing a
Stack from
and to the filesystem.
- org.anchoranalysis.image.io.stack.input - package org.anchoranalysis.image.io.stack.input
-
Non-bean classes for reading a
Stack from the
filesystem.
- org.anchoranalysis.image.io.stack.output - package org.anchoranalysis.image.io.stack.output
-
Non-bean classes for writing a
Stack to the
filesystem.
- org.anchoranalysis.image.io.stack.output.box - package org.anchoranalysis.image.io.stack.output.box
-
Base classes for generators that ultimately write
only a bounding-box portion of a
Stack to the filesystem.
- org.anchoranalysis.image.io.stack.output.generator - package org.anchoranalysis.image.io.stack.output.generator
-
Base classes for generators that ultimately write a
Stack to the filesystem.
- org.anchoranalysis.image.io.stack.time - package org.anchoranalysis.image.io.stack.time
-
A time-sequence of
Stacks.
- org.anchoranalysis.image.voxel - package org.anchoranalysis.image.voxel
-
Data-structures to store and manipulate image raster-data or voxels.
- org.anchoranalysis.image.voxel.arithmetic - package org.anchoranalysis.image.voxel.arithmetic
-
Arithmetic operations for
Voxels.
- org.anchoranalysis.image.voxel.assigner - package org.anchoranalysis.image.voxel.assigner
-
Assigns values to some or all voxels.
- org.anchoranalysis.image.voxel.binary - package org.anchoranalysis.image.voxel.binary
-
- org.anchoranalysis.image.voxel.binary.connected - package org.anchoranalysis.image.voxel.binary.connected
-
- org.anchoranalysis.image.voxel.binary.values - package org.anchoranalysis.image.voxel.binary.values
-
Defining on and off intensity-values to interpret an image in a binary way.
- org.anchoranalysis.image.voxel.buffer - package org.anchoranalysis.image.voxel.buffer
-
A buffer of voxel-values, usually corresponding to a single z-slice in
Voxels.
- org.anchoranalysis.image.voxel.buffer.max - package org.anchoranalysis.image.voxel.buffer.max
-
- org.anchoranalysis.image.voxel.buffer.mean - package org.anchoranalysis.image.voxel.buffer.mean
-
Buffer for performing a mean intensity projection.
- org.anchoranalysis.image.voxel.buffer.primitive - package org.anchoranalysis.image.voxel.buffer.primitive
-
Conversion of both primitive data types and image structures between Anchor's data-structures and
other representations.
- org.anchoranalysis.image.voxel.buffer.slice - package org.anchoranalysis.image.voxel.buffer.slice
-
A container with voxel-buffers for each z-slice.
- org.anchoranalysis.image.voxel.convert - package org.anchoranalysis.image.voxel.convert
-
Converting
Voxels to different data-types.
- org.anchoranalysis.image.voxel.convert.bufferedimage - package org.anchoranalysis.image.voxel.convert.bufferedimage
-
- org.anchoranalysis.image.voxel.convert.imglib2 - package org.anchoranalysis.image.voxel.convert.imglib2
-
Converts anchor data-structures to those used by
ImgLib2.
- org.anchoranalysis.image.voxel.datatype - package org.anchoranalysis.image.voxel.datatype
-
The different data-types that can be used to represent voxels.
- org.anchoranalysis.image.voxel.extracter - package org.anchoranalysis.image.voxel.extracter
-
Methods to read/copy/duplicate portions of voxels.
- org.anchoranalysis.image.voxel.extracter.predicate - package org.anchoranalysis.image.voxel.extracter.predicate
-
Methods to find or count voxels that satisfy a predicate.
- org.anchoranalysis.image.voxel.factory - package org.anchoranalysis.image.voxel.factory
-
- org.anchoranalysis.image.voxel.interpolator - package org.anchoranalysis.image.voxel.interpolator
-
Different interpolator methods to use when scaling voxels.
- org.anchoranalysis.image.voxel.iterator - package org.anchoranalysis.image.voxel.iterator
-
Utilities to iterate over voxel-locations in images and sub-regions of images.
- org.anchoranalysis.image.voxel.iterator.intersecting - package org.anchoranalysis.image.voxel.iterator.intersecting
-
Like org.anchoranalysis.image.voxel.iterator but refers to iterators that operation over
the intersecting regions of two entities.
- org.anchoranalysis.image.voxel.iterator.neighbor - package org.anchoranalysis.image.voxel.iterator.neighbor
-
Iterating over a point's neighboring voxels.
- org.anchoranalysis.image.voxel.iterator.neighbor.kernel - package org.anchoranalysis.image.voxel.iterator.neighbor.kernel
-
- org.anchoranalysis.image.voxel.iterator.predicate - package org.anchoranalysis.image.voxel.iterator.predicate
-
Functional-interfaces for processing different combinations of points and buffers that return a
boolean.
- org.anchoranalysis.image.voxel.iterator.process - package org.anchoranalysis.image.voxel.iterator.process
-
Functional-interfaces for processing different combinations of points and buffers that do not
return a value.
- org.anchoranalysis.image.voxel.iterator.process.buffer - package org.anchoranalysis.image.voxel.iterator.process.buffer
-
Functional-interfaces for processing different combinations of points and raw buffers, but not
VoxelBuffer.
- org.anchoranalysis.image.voxel.iterator.process.voxelbuffer - package org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
-
Functional-interfaces for processing different combinations of points and
VoxelBuffer but not raw buffers.
- org.anchoranalysis.image.voxel.kernel - package org.anchoranalysis.image.voxel.kernel
-
Applying a
kernel via
convolution to voxels.
- org.anchoranalysis.image.voxel.kernel.count - package org.anchoranalysis.image.voxel.kernel.count
-
Kernels to count the number of voxels that are equal to a particular value.
- org.anchoranalysis.image.voxel.kernel.morphological - package org.anchoranalysis.image.voxel.kernel.morphological
-
Kernels that apply morphological operations.
- org.anchoranalysis.image.voxel.kernel.outline - package org.anchoranalysis.image.voxel.kernel.outline
-
Kernel to find outline voxels on an object.
- org.anchoranalysis.image.voxel.neighborhood - package org.anchoranalysis.image.voxel.neighborhood
-
A region in proximity to a voxel, encompassing this voxel as well as others.
- org.anchoranalysis.image.voxel.object - package org.anchoranalysis.image.voxel.object
-
The fundamental data class that is an
ObjectMask
and related structures.
- org.anchoranalysis.image.voxel.object.morphological - package org.anchoranalysis.image.voxel.object.morphological
-
- org.anchoranalysis.image.voxel.object.morphological.predicate - package org.anchoranalysis.image.voxel.object.morphological.predicate
-
Predicates to match certain voxels as used in org.anchoranalysis.image.voxel.object.morphological.
- org.anchoranalysis.image.voxel.statistics - package org.anchoranalysis.image.voxel.statistics
-
Statistics about aggregated voxel intensities.
- org.anchoranalysis.image.voxel.thresholder - package org.anchoranalysis.image.voxel.thresholder
-
Thresholding operations on voxels.
- org.anchoranalysis.io.bioformats - package org.anchoranalysis.io.bioformats
-
Non-bean classes for filesystem I/O using
Bioformats.
- org.anchoranalysis.io.bioformats.bean - package org.anchoranalysis.io.bioformats.bean
-
- org.anchoranalysis.io.bioformats.bean.options - package org.anchoranalysis.io.bioformats.bean.options
-
User-specified options that can modify metadata or other attributes of a loaded Bioformats image.
- org.anchoranalysis.io.bioformats.bean.writer - package org.anchoranalysis.io.bioformats.bean.writer
-
Writing stacks to the file system using the Bioformats library.
- org.anchoranalysis.io.bioformats.copyconvert - package org.anchoranalysis.io.bioformats.copyconvert
-
Converts the byte stream opened by Bioformats into channels of particular data-type.
- org.anchoranalysis.io.bioformats.copyconvert.tobyte - package org.anchoranalysis.io.bioformats.copyconvert.tobyte
-
Converts the byte stream opened by Bioformats into channels of
ByteBuffer.
- org.anchoranalysis.io.bioformats.copyconvert.tofloat - package org.anchoranalysis.io.bioformats.copyconvert.tofloat
-
Converts the byte stream opened by Bioformats into channels of
FloatBuffer.
- org.anchoranalysis.io.bioformats.copyconvert.toint - package org.anchoranalysis.io.bioformats.copyconvert.toint
-
Converts the byte stream opened by Bioformats into channels of
IntBuffer.
- org.anchoranalysis.io.bioformats.copyconvert.toshort - package org.anchoranalysis.io.bioformats.copyconvert.toshort
-
Converts the byte stream opened by Bioformats into channels of
ShortBuffer.
- org.anchoranalysis.io.bioformats.metadata - package org.anchoranalysis.io.bioformats.metadata
-
Reading metadata information from files using EXIF and/or other metadata headers.
- org.anchoranalysis.io.generator - package org.anchoranalysis.io.generator
-
Base-classes and utilities for generators, which write different types of objects to the file
system.
- org.anchoranalysis.io.generator.collection - package org.anchoranalysis.io.generator.collection
-
Outputting more than one element collectively using a generator.
- org.anchoranalysis.io.generator.combined - package org.anchoranalysis.io.generator.combined
-
Combining multiple generators into one.
- org.anchoranalysis.io.generator.sequence - package org.anchoranalysis.io.generator.sequence
-
Writing a sequence of elements using a generator.
- org.anchoranalysis.io.generator.sequence.pattern - package org.anchoranalysis.io.generator.sequence.pattern
-
A particular naming pattern files follow when outputted.
- org.anchoranalysis.io.generator.serialized - package org.anchoranalysis.io.generator.serialized
-
Generators for writing serialized objects.
- org.anchoranalysis.io.generator.tabular - package org.anchoranalysis.io.generator.tabular
-
Generators for writing tabular data, including CSV.
- org.anchoranalysis.io.generator.text - package org.anchoranalysis.io.generator.text
-
Generators for writing textual data, including strings.
- org.anchoranalysis.io.generator.xml - package org.anchoranalysis.io.generator.xml
-
Generators for writing XML data.
- org.anchoranalysis.io.imagej.bean - package org.anchoranalysis.io.imagej.bean
-
- org.anchoranalysis.io.imagej.bean.stack.writer - package org.anchoranalysis.io.imagej.bean.stack.writer
-
Raster-writers that use ImageJ to write images to the filesystem.
- org.anchoranalysis.io.imagej.convert - package org.anchoranalysis.io.imagej.convert
-
Converts to and from ImageJ data-structures for images.
- org.anchoranalysis.io.imagej.interpolator - package org.anchoranalysis.io.imagej.interpolator
-
Image interpolation when scaling using ImageJ.
- org.anchoranalysis.io.input - package org.anchoranalysis.io.input
-
Classes relating to creating inputs for an experiment / task.
- org.anchoranalysis.io.input.bean - package org.anchoranalysis.io.input.bean
-
Beans related to collecting inputs from the file-system for an experiment.
- org.anchoranalysis.io.input.bean.dictionary - package org.anchoranalysis.io.input.bean.dictionary
-
- org.anchoranalysis.io.input.bean.files - package org.anchoranalysis.io.input.bean.files
-
Methods to provide a collection of
Files.
- org.anchoranalysis.io.input.bean.namer - package org.anchoranalysis.io.input.bean.namer
-
Beans to derive names (compact unique identifiers) from files.
- org.anchoranalysis.io.input.bean.path - package org.anchoranalysis.io.input.bean.path
-
Beans pertaining to manipulating and matching against file-paths.
- org.anchoranalysis.io.input.bean.path.matcher - package org.anchoranalysis.io.input.bean.path.matcher
-
Beans to find a subset of files that match a particular conditions on their paths.
- org.anchoranalysis.io.input.bean.path.provider - package org.anchoranalysis.io.input.bean.path.provider
-
Methods to provide a single file-path.
- org.anchoranalysis.io.input.csv - package org.anchoranalysis.io.input.csv
-
Classes for reading comma-separated-values (CSV) files.
- org.anchoranalysis.io.input.file - package org.anchoranalysis.io.input.file
-
Non-bean classes that relate to using files during inputting.
- org.anchoranalysis.io.input.path - package org.anchoranalysis.io.input.path
-
Non-bean classes pertaining to getting/extracting/manipulating paths as used in inputting.
- org.anchoranalysis.io.input.path.matcher - package org.anchoranalysis.io.input.path.matcher
-
Non-bean classes to help with org.anchoranalysis.io.input.bean.path.matcher.
- org.anchoranalysis.io.manifest - package org.anchoranalysis.io.manifest
-
A manifest that records what outputs occur and where they occur.
- org.anchoranalysis.io.manifest.deserializer - package org.anchoranalysis.io.manifest.deserializer
-
Classes to read manifests from the file-system.
- org.anchoranalysis.io.manifest.directory - package org.anchoranalysis.io.manifest.directory
-
Entities to indicate a directory in the manifest.
- org.anchoranalysis.io.manifest.directory.sequenced - package org.anchoranalysis.io.manifest.directory.sequenced
-
Classes related to a directory that has a particular sequence of outputted filenames.
- org.anchoranalysis.io.manifest.file - package org.anchoranalysis.io.manifest.file
-
Entities to indicate a file and its role in the manifest.
- org.anchoranalysis.io.manifest.finder - package org.anchoranalysis.io.manifest.finder
-
Methods to search through a manifest-file to find outputs matching certain conditions.
- org.anchoranalysis.io.manifest.finder.match - package org.anchoranalysis.io.manifest.finder.match
-
Predicates that are useful for matching against particular type of objects in finders.
- org.anchoranalysis.io.manifest.operationrecorder - package org.anchoranalysis.io.manifest.operationrecorder
-
Makes a record of each file/subdirectory written as output.
- org.anchoranalysis.io.manifest.sequencetype - package org.anchoranalysis.io.manifest.sequencetype
-
Predictable patterns of indexes as used in sets of outputted files.
- org.anchoranalysis.io.output.bean - package org.anchoranalysis.io.output.bean
-
Beans for the framework around writing files to the file-system.
- org.anchoranalysis.io.output.bean.enabled - package org.anchoranalysis.io.output.bean.enabled
-
Beans indicating whether a particular output is enabled or not.
- org.anchoranalysis.io.output.bean.path.prefixer - package org.anchoranalysis.io.output.bean.path.prefixer
-
Beans for generating paths for outputting files by adding a prefix, suffix etc.
- org.anchoranalysis.io.output.bean.rules - package org.anchoranalysis.io.output.bean.rules
-
Rules for determining if a particular output is enabled or not in a context of a hierarchy.
- org.anchoranalysis.io.output.enabled - package org.anchoranalysis.io.output.enabled
-
Non-beans pertaining to whether a particular output is enabled or not.
- org.anchoranalysis.io.output.enabled.multi - package org.anchoranalysis.io.output.enabled.multi
-
Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
- org.anchoranalysis.io.output.enabled.single - package org.anchoranalysis.io.output.enabled.single
-
Non-beans that pertain to whether a single level has outputs that are enabled or not.
- org.anchoranalysis.io.output.error - package org.anchoranalysis.io.output.error
-
Exceptions that may be thrown when writing files to the file-system.
- org.anchoranalysis.io.output.namestyle - package org.anchoranalysis.io.output.namestyle
-
Methods of naming a file with an index in the file-name.
- org.anchoranalysis.io.output.outputter - package org.anchoranalysis.io.output.outputter
-
Classes for outputting to particular directories.
- org.anchoranalysis.io.output.outputter.directory - package org.anchoranalysis.io.output.outputter.directory
-
BoundDirectory and related classes.
- org.anchoranalysis.io.output.path.prefixer - package org.anchoranalysis.io.output.path.prefixer
-
Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
- org.anchoranalysis.io.output.recorded - package org.anchoranalysis.io.output.recorded
-
Classes for recording the output-names used as they are written / queried.
- org.anchoranalysis.io.output.writer - package org.anchoranalysis.io.output.writer
-
Allows a generators to write element(s) to the filesystem.
- org.anchoranalysis.io.output.xml - package org.anchoranalysis.io.output.xml
-
Outputting XML to the file-system.
- org.anchoranalysis.launcher - package org.anchoranalysis.launcher
-
Parent package and entry-point classes for the Anchor command-line launcher application.
- org.anchoranalysis.launcher.config - package org.anchoranalysis.launcher.config
-
Specifies a configuration of the launcher for a particular application.
- org.anchoranalysis.launcher.executor - package org.anchoranalysis.launcher.executor
-
Runs a particular experiment after identifying necessary paths and input files.
- org.anchoranalysis.launcher.executor.selectparam - package org.anchoranalysis.launcher.executor.selectparam
-
Different methods of selecting a object T that is used as a parameter for an experiment.
- org.anchoranalysis.launcher.executor.selectparam.experiment - package org.anchoranalysis.launcher.executor.selectparam.experiment
-
- org.anchoranalysis.launcher.executor.selectparam.path - package org.anchoranalysis.launcher.executor.selectparam.path
-
SelectParams for loading a
Optional<Path> for inputs, outputs or tasks.
- org.anchoranalysis.launcher.executor.selectparam.path.convert - package org.anchoranalysis.launcher.executor.selectparam.path.convert
-
Converting paths to/from different formats as needed by org.anchoranalysis.launcher.executor.selectparam.path.
- org.anchoranalysis.launcher.options - package org.anchoranalysis.launcher.options
-
A centralized location for all command-line options used by the launcher.
- org.anchoranalysis.launcher.options.process - package org.anchoranalysis.launcher.options.process
-
Adding/removing/changing the arguments (input and output) from the experiment via
command-line-options.
- org.anchoranalysis.launcher.resources - package org.anchoranalysis.launcher.resources
-
Reading and integrating resources for the launcher.
- org.anchoranalysis.launcher.run - package org.anchoranalysis.launcher.run
-
Parses command-line arguments and runs an experiment.
- org.anchoranalysis.launcher.run.tasks - package org.anchoranalysis.launcher.run.tasks
-
Loading and displaying pre-defined tasks.
- org.anchoranalysis.math.arithmetic - package org.anchoranalysis.math.arithmetic
-
Performing primitive type conversion, counting and summing.
- org.anchoranalysis.math.equation - package org.anchoranalysis.math.equation
-
Solving or manipulating equations.
- org.anchoranalysis.math.histogram - package org.anchoranalysis.math.histogram
-
The
Histogram data class and related operations.
- org.anchoranalysis.math.optimization - package org.anchoranalysis.math.optimization
-
- org.anchoranalysis.math.relation - package org.anchoranalysis.math.relation
-
Different kinds of binary-relations.
- org.anchoranalysis.math.statistics - package org.anchoranalysis.math.statistics
-
Data structures and algorithms to calculate statistics.
- org.anchoranalysis.math.statistics.moment - package org.anchoranalysis.math.statistics.moment
-
Calculates first and second
image
moments from a covariance matrix of points.
- org.anchoranalysis.mpp.bean - package org.anchoranalysis.mpp.bean
-
- org.anchoranalysis.mpp.bean.bound - package org.anchoranalysis.mpp.bean.bound
-
Lower and upper limits set around variables.
- org.anchoranalysis.mpp.bean.bound.rotation - package org.anchoranalysis.mpp.bean.bound.rotation
-
Bounds on how to rotate an entity in Euclidean space.
- org.anchoranalysis.mpp.bean.mark - package org.anchoranalysis.mpp.bean.mark
-
Beans generally related to
Marks.
- org.anchoranalysis.mpp.bean.mark.factory - package org.anchoranalysis.mpp.bean.mark.factory
-
Beans related to creating
Marks.
- org.anchoranalysis.mpp.bean.points - package org.anchoranalysis.mpp.bean.points
-
Operations based on sets of points.
- org.anchoranalysis.mpp.bean.points.fitter - package org.anchoranalysis.mpp.bean.points.fitter
-
Fitting structures to sets of points.
- org.anchoranalysis.mpp.bean.proposer - package org.anchoranalysis.mpp.bean.proposer
-
Proposing
Marks or other data-structures with particular
attributes.
- org.anchoranalysis.mpp.bean.provider - package org.anchoranalysis.mpp.bean.provider
-
- org.anchoranalysis.mpp.bean.regionmap - package org.anchoranalysis.mpp.bean.regionmap
-
Voxel subregions of
Marks.
- org.anchoranalysis.mpp.feature.addcriteria - package org.anchoranalysis.mpp.feature.addcriteria
-
Criteria for adding edges during optimization of marked-point-processes.
- org.anchoranalysis.mpp.feature.bean.energy.element - package org.anchoranalysis.mpp.feature.bean.energy.element
-
Implementations and helper classes for calculating energy during an energy-minimization
optimization scheme.
- org.anchoranalysis.mpp.feature.bean.energy.scheme - package org.anchoranalysis.mpp.feature.bean.energy.scheme
-
- org.anchoranalysis.mpp.feature.bean.mark - package org.anchoranalysis.mpp.feature.bean.mark
-
Features calculated on a
Mark.
- org.anchoranalysis.mpp.feature.bean.mark.collection - package org.anchoranalysis.mpp.feature.bean.mark.collection
-
Features calculated on a org.anchoranalysis.mpp.feature.bean.mark.collection.
- org.anchoranalysis.mpp.feature.energy - package org.anchoranalysis.mpp.feature.energy
-
Non-bean classes pertaining to calculating energy during an energy-minimization optimization
scheme.
- org.anchoranalysis.mpp.feature.energy.marks - package org.anchoranalysis.mpp.feature.energy.marks
-
Non-bean classes pertaining to calculating energy of {org.anchoranalysis.mpp.mark.Mark}s.
- org.anchoranalysis.mpp.feature.energy.saved - package org.anchoranalysis.mpp.feature.energy.saved
-
Saved snapshots of energy-calculations.
- org.anchoranalysis.mpp.feature.energy.scheme - package org.anchoranalysis.mpp.feature.energy.scheme
-
Factorized form of storing the energy during an energy-minimization optimization scheme.
- org.anchoranalysis.mpp.feature.error - package org.anchoranalysis.mpp.feature.error
-
Exceptions relating to
Features involving classes from
anchor-mpp.
- org.anchoranalysis.mpp.feature.input - package org.anchoranalysis.mpp.feature.input
-
Inputs to mark-point-processes related
Features.
- org.anchoranalysis.mpp.feature.mark - package org.anchoranalysis.mpp.feature.mark
-
Non-bean classes for calculating feature-values related to
Marks.
- org.anchoranalysis.mpp.index - package org.anchoranalysis.mpp.index
-
Indexing voxel-values in different ways.
- org.anchoranalysis.mpp.index.factory - package org.anchoranalysis.mpp.index.factory
-
Factories for classes in org.anchoranalysis.mpp.index.
- org.anchoranalysis.mpp.init - package org.anchoranalysis.mpp.init
-
Parameters used to initialize certain types of beans.
- org.anchoranalysis.mpp.io.bean.input - package org.anchoranalysis.mpp.io.bean.input
-
Beans for reading data structures related to marked point processes from the file system.
- org.anchoranalysis.mpp.io.bean.report.feature - package org.anchoranalysis.mpp.io.bean.report.feature
-
Beans for communicating feature-values from data-structures in human-readable manner.
- org.anchoranalysis.mpp.io.input - package org.anchoranalysis.mpp.io.input
-
Non-beans for reading data structures related to marked point processes from the file system.
- org.anchoranalysis.mpp.io.marks - package org.anchoranalysis.mpp.io.marks
-
Non-beans to help write visualization of
Marks to the
filesystem.
- org.anchoranalysis.mpp.io.marks.generator - package org.anchoranalysis.mpp.io.marks.generator
-
Generator base classes to help write visualization of
Marks to the filesystem.
- org.anchoranalysis.mpp.io.output - package org.anchoranalysis.mpp.io.output
-
Non-beans for writing data structures related to marked point processes from the file system.
- org.anchoranalysis.mpp.mark - package org.anchoranalysis.mpp.mark
-
Non-bean classes related to
Marks.
- org.anchoranalysis.mpp.mark.conic - package org.anchoranalysis.mpp.mark.conic
-
- org.anchoranalysis.mpp.mark.points - package org.anchoranalysis.mpp.mark.points
-
Marks implementing structures based on points.
- org.anchoranalysis.mpp.mark.voxelized - package org.anchoranalysis.mpp.mark.voxelized
-
A mark after a voxel-representation has been inferred.
- org.anchoranalysis.mpp.mark.voxelized.memo - package org.anchoranalysis.mpp.mark.voxelized.memo
-
- org.anchoranalysis.mpp.overlap - package org.anchoranalysis.mpp.overlap
-
Calculating overlaps between two
Marks.
- org.anchoranalysis.mpp.overlay - package org.anchoranalysis.mpp.overlay
-
- org.anchoranalysis.mpp.pair - package org.anchoranalysis.mpp.pair
-
- org.anchoranalysis.mpp.proposer - package org.anchoranalysis.mpp.proposer
-
Non-bean classes for proposing
Marks or other data-structures
with particular attributes.
- org.anchoranalysis.mpp.proposer.error - package org.anchoranalysis.mpp.proposer.error
-
Recording errors related to proposing
Marks or other
data-structures with particular attributes.
- org.anchoranalysis.mpp.segment.bean - package org.anchoranalysis.mpp.segment.bean
-
Beans for segmentation algorithms related to marked-point-processes.
- org.anchoranalysis.mpp.segment.bean.define - package org.anchoranalysis.mpp.segment.bean.define
-
- org.anchoranalysis.mpp.segment.bean.optimization - package org.anchoranalysis.mpp.segment.bean.optimization
-
Schemes for finding optima (minima or maxima) via optimization.
- org.anchoranalysis.mpp.segment.bean.optimization.feedback - package org.anchoranalysis.mpp.segment.bean.optimization.feedback
-
- org.anchoranalysis.mpp.segment.bean.optimization.kernel - package org.anchoranalysis.mpp.segment.bean.optimization.kernel
-
Base classes for kernels that transition a configuration of marks (a
MarkCollection) into an altered version.
- org.anchoranalysis.mpp.segment.bean.optimization.termination - package org.anchoranalysis.mpp.segment.bean.optimization.termination
-
- org.anchoranalysis.mpp.segment.define - package org.anchoranalysis.mpp.segment.define
-
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.define.
- org.anchoranalysis.mpp.segment.optimization - package org.anchoranalysis.mpp.segment.optimization
-
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.
- org.anchoranalysis.mpp.segment.optimization.feedback - package org.anchoranalysis.mpp.segment.optimization.feedback
-
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.feedback.
- org.anchoranalysis.mpp.segment.optimization.feedback.aggregate - package org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
-
Aggregating optimization feedback over time.
- org.anchoranalysis.mpp.segment.optimization.feedback.period - package org.anchoranalysis.mpp.segment.optimization.feedback.period
-
Collecting optimization feedback periodically.
- org.anchoranalysis.mpp.segment.optimization.kernel - package org.anchoranalysis.mpp.segment.optimization.kernel
-
Non-bean classes used in org.anchoranalysis.mpp.segment.bean.optimization.kernel.
- org.anchoranalysis.mpp.segment.optimization.step - package org.anchoranalysis.mpp.segment.optimization.step
-
Describes an individual step in the optimization.
- org.anchoranalysis.mpp.segment.transformer - package org.anchoranalysis.mpp.segment.transformer
-
Mapping one type of optimization state to another.
- org.anchoranalysis.overlay - package org.anchoranalysis.overlay
-
Overlays and related classes involving drawing entities on top
of an image.
- org.anchoranalysis.overlay.bean - package org.anchoranalysis.overlay.bean
-
Beans relating to drawing an
Overlay on an image.
- org.anchoranalysis.overlay.collection - package org.anchoranalysis.overlay.collection
-
- org.anchoranalysis.overlay.identifier - package org.anchoranalysis.overlay.identifier
-
- org.anchoranalysis.overlay.object - package org.anchoranalysis.overlay.object
-
- org.anchoranalysis.overlay.object.scaled - package org.anchoranalysis.overlay.object.scaled
-
Creates a scaled version of
ObjectMask to use as an
overlay.
- org.anchoranalysis.overlay.writer - package org.anchoranalysis.overlay.writer
-
Drawing an overlay on an image.
- org.anchoranalysis.plot - package org.anchoranalysis.plot
-
Plotting data on charts.
- org.anchoranalysis.plot.bean - package org.anchoranalysis.plot.bean
-
Beans for plotting.
- org.anchoranalysis.plot.bean.colorscheme - package org.anchoranalysis.plot.bean.colorscheme
-
Color schemes associated with plots.
- org.anchoranalysis.plot.index - package org.anchoranalysis.plot.index
-
Non-bean plot definitions.
- org.anchoranalysis.plugin.annotation.bean.aggregate - package org.anchoranalysis.plugin.annotation.bean.aggregate
-
Beans to combine two or more annotations.
- org.anchoranalysis.plugin.annotation.bean.comparer - package org.anchoranalysis.plugin.annotation.bean.comparer
-
Comparing the similarity of annotations from two images to each other.
- org.anchoranalysis.plugin.annotation.bean.comparison - package org.anchoranalysis.plugin.annotation.bean.comparison
-
Task to compare a set of annotations to a segmentation or another set of annotations.
- org.anchoranalysis.plugin.annotation.bean.comparison.assigner - package org.anchoranalysis.plugin.annotation.bean.comparison.assigner
-
Pairs annotations from two different sets, creating an assignment of some type.
- org.anchoranalysis.plugin.annotation.bean.file - package org.anchoranalysis.plugin.annotation.bean.file
-
- org.anchoranalysis.plugin.annotation.bean.label - package org.anchoranalysis.plugin.annotation.bean.label
-
A label as used for annotating.
- org.anchoranalysis.plugin.annotation.bean.strategy - package org.anchoranalysis.plugin.annotation.bean.strategy
-
Strategies for how to annotate an image, such label per image etc.
- org.anchoranalysis.plugin.annotation.comparison - package org.anchoranalysis.plugin.annotation.comparison
-
Non-bean classes for comparing two sets of annotations.
- org.anchoranalysis.plugin.annotation.counter - package org.anchoranalysis.plugin.annotation.counter
-
Utility classes for counting images incrementally.
- org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction - package org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
-
Morphological grayscale-reconstruction algorithm.
- org.anchoranalysis.plugin.fiji.bean.channel.provider - package org.anchoranalysis.plugin.fiji.bean.channel.provider
-
- org.anchoranalysis.plugin.fiji.bean.channel.provider.distance - package org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
-
- org.anchoranalysis.plugin.fiji.bean.define - package org.anchoranalysis.plugin.fiji.bean.define
-
- org.anchoranalysis.plugin.fiji.bean.mask.provider - package org.anchoranalysis.plugin.fiji.bean.mask.provider
-
- org.anchoranalysis.plugin.fiji.bean.threshold - package org.anchoranalysis.plugin.fiji.bean.threshold
-
- org.anchoranalysis.plugin.image.bean.blur - package org.anchoranalysis.plugin.image.bean.blur
-
Filters that perform blurring.
- org.anchoranalysis.plugin.image.bean.channel.convert - package org.anchoranalysis.plugin.image.bean.channel.convert
-
- org.anchoranalysis.plugin.image.bean.channel.provider - package org.anchoranalysis.plugin.image.bean.channel.provider
-
Implementations of
ChannelProvider that are
generic base-classes or otherwise abstract or general.
- org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic - package org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- org.anchoranalysis.plugin.image.bean.channel.provider.assign - package org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
- org.anchoranalysis.plugin.image.bean.channel.provider.convert - package org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
- org.anchoranalysis.plugin.image.bean.channel.provider.gradient - package org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Implementations of
ChannelProvider that calculate
the gradient of a
Channel's voxels in one or more
dimensions.
- org.anchoranalysis.plugin.image.bean.channel.provider.intensity - package org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
- org.anchoranalysis.plugin.image.bean.channel.provider.mask - package org.anchoranalysis.plugin.image.bean.channel.provider.mask
-
- org.anchoranalysis.plugin.image.bean.channel.provider.object - package org.anchoranalysis.plugin.image.bean.channel.provider.object
-
- org.anchoranalysis.plugin.image.bean.channel.provider.score - package org.anchoranalysis.plugin.image.bean.channel.provider.score
-
Implementations of
ChannelProvider that assign a
score to particular subregions of a channel.
- org.anchoranalysis.plugin.image.bean.channel.provider.slice - package org.anchoranalysis.plugin.image.bean.channel.provider.slice
-
Implementations of
ChannelProvider that process 3D
channels slice-by-slice.
- org.anchoranalysis.plugin.image.bean.color.provider - package org.anchoranalysis.plugin.image.bean.color.provider
-
- org.anchoranalysis.plugin.image.bean.dictionary - package org.anchoranalysis.plugin.image.bean.dictionary
-
- org.anchoranalysis.plugin.image.bean.dimensions.provider - package org.anchoranalysis.plugin.image.bean.dimensions.provider
-
- org.anchoranalysis.plugin.image.bean.histogram.provider - package org.anchoranalysis.plugin.image.bean.histogram.provider
-
- org.anchoranalysis.plugin.image.bean.histogram.threshold - package org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Thresholding of intensity values represented in at
Histogram.
- org.anchoranalysis.plugin.image.bean.mask.provider - package org.anchoranalysis.plugin.image.bean.mask.provider
-
- org.anchoranalysis.plugin.image.bean.mask.provider.combine - package org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Implementations of
MaskProvider that combine
existing providers.
- org.anchoranalysis.plugin.image.bean.mask.provider.convert - package org.anchoranalysis.plugin.image.bean.mask.provider.convert
-
- org.anchoranalysis.plugin.image.bean.mask.provider.morphological - package org.anchoranalysis.plugin.image.bean.mask.provider.morphological
-
Implementations of
MaskProvider that implement
morphological operations.
- org.anchoranalysis.plugin.image.bean.mask.provider.predicate - package org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
- org.anchoranalysis.plugin.image.bean.mask.provider.segment - package org.anchoranalysis.plugin.image.bean.mask.provider.segment
-
- org.anchoranalysis.plugin.image.bean.mask.provider.slice - package org.anchoranalysis.plugin.image.bean.mask.provider.slice
-
Implementations of
MaskProvider that process 3D
masks slice-by-slice.
- org.anchoranalysis.plugin.image.bean.object.filter - package org.anchoranalysis.plugin.image.bean.object.filter
-
- org.anchoranalysis.plugin.image.bean.object.filter.collective - package org.anchoranalysis.plugin.image.bean.object.filter.collective
-
Implementations of
ObjectFilter that assess each
element in a collection
collectively.
- org.anchoranalysis.plugin.image.bean.object.filter.combine - package org.anchoranalysis.plugin.image.bean.object.filter.combine
-
- org.anchoranalysis.plugin.image.bean.object.filter.independent - package org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Implementations of
ObjectFilter that
independently assess each element in a collection.
- org.anchoranalysis.plugin.image.bean.object.match - package org.anchoranalysis.plugin.image.bean.object.match
-
- org.anchoranalysis.plugin.image.bean.object.provider - package org.anchoranalysis.plugin.image.bean.object.provider
-
- org.anchoranalysis.plugin.image.bean.object.provider.connected - package org.anchoranalysis.plugin.image.bean.object.provider.connected
-
- org.anchoranalysis.plugin.image.bean.object.provider.feature - package org.anchoranalysis.plugin.image.bean.object.provider.feature
-
- org.anchoranalysis.plugin.image.bean.object.provider.filter - package org.anchoranalysis.plugin.image.bean.object.provider.filter
-
- org.anchoranalysis.plugin.image.bean.object.provider.mask - package org.anchoranalysis.plugin.image.bean.object.provider.mask
-
- org.anchoranalysis.plugin.image.bean.object.provider.merge - package org.anchoranalysis.plugin.image.bean.object.provider.merge
-
- org.anchoranalysis.plugin.image.bean.object.provider.morphological - package org.anchoranalysis.plugin.image.bean.object.provider.morphological
-
- org.anchoranalysis.plugin.image.bean.object.provider.segment - package org.anchoranalysis.plugin.image.bean.object.provider.segment
-
- org.anchoranalysis.plugin.image.bean.object.provider.slice - package org.anchoranalysis.plugin.image.bean.object.provider.slice
-
- org.anchoranalysis.plugin.image.bean.object.provider.split - package org.anchoranalysis.plugin.image.bean.object.provider.split
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel - package org.anchoranalysis.plugin.image.bean.object.segment.channel
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
-
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
-
- org.anchoranalysis.plugin.image.bean.object.segment.reduce - package org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Strategies for reducing the number of elements with a list by merging/removing lower-confidence
elements that overlap.
- org.anchoranalysis.plugin.image.bean.scale - package org.anchoranalysis.plugin.image.bean.scale
-
Implementations of
ScaleCalculator for calculating
a scaling-factor from dimensions.
- org.anchoranalysis.plugin.image.bean.segment.binary - package org.anchoranalysis.plugin.image.bean.segment.binary
-
- org.anchoranalysis.plugin.image.bean.stack.provider - package org.anchoranalysis.plugin.image.bean.stack.provider
-
- org.anchoranalysis.plugin.image.bean.stack.provider.color - package org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Implementations of
StackProvider that color
portions of an image.
- org.anchoranalysis.plugin.image.bean.stack.provider.plot - package org.anchoranalysis.plugin.image.bean.stack.provider.plot
-
- org.anchoranalysis.plugin.image.bean.thumbnail.object - package org.anchoranalysis.plugin.image.bean.thumbnail.object
-
- org.anchoranalysis.plugin.image.bean.thumbnail.stack - package org.anchoranalysis.plugin.image.bean.thumbnail.stack
-
- org.anchoranalysis.plugin.image.channel - package org.anchoranalysis.plugin.image.channel
-
Non-beans for operations or calculations relating to
Channels.
- org.anchoranalysis.plugin.image.feature.bean.dimensions - package org.anchoranalysis.plugin.image.feature.bean.dimensions
-
- org.anchoranalysis.plugin.image.feature.bean.histogram.statistic - package org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- org.anchoranalysis.plugin.image.feature.bean.histogram.threshold - package org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
-
- org.anchoranalysis.plugin.image.feature.bean.list - package org.anchoranalysis.plugin.image.feature.bean.list
-
- org.anchoranalysis.plugin.image.feature.bean.list.pair - package org.anchoranalysis.plugin.image.feature.bean.list.pair
-
- org.anchoranalysis.plugin.image.feature.bean.list.permute - package org.anchoranalysis.plugin.image.feature.bean.list.permute
-
- org.anchoranalysis.plugin.image.feature.bean.metadata - package org.anchoranalysis.plugin.image.feature.bean.metadata
-
- org.anchoranalysis.plugin.image.feature.bean.morphological - package org.anchoranalysis.plugin.image.feature.bean.morphological
-
- org.anchoranalysis.plugin.image.feature.bean.object.collection - package org.anchoranalysis.plugin.image.feature.bean.object.collection
-
- org.anchoranalysis.plugin.image.feature.bean.object.combine - package org.anchoranalysis.plugin.image.feature.bean.object.combine
-
- org.anchoranalysis.plugin.image.feature.bean.object.pair - package org.anchoranalysis.plugin.image.feature.bean.object.pair
-
- org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap - package org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
Features that calculate the degree of overlap between two
ObjectMasks.
- org.anchoranalysis.plugin.image.feature.bean.object.pair.touching - package org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
-
Features that calculate how many other objects an
ObjectMask directly neighbors.
- org.anchoranalysis.plugin.image.feature.bean.object.single - package org.anchoranalysis.plugin.image.feature.bean.object.single
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.border - package org.anchoranalysis.plugin.image.feature.bean.object.single.border
-
Implementations of
FeatureSingleObject that determine if an
object lies at the border of an image.
- org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox - package org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.energy - package org.anchoranalysis.plugin.image.feature.bean.object.single.energy
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.intensity - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.moments - package org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.morphological - package org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.shape - package org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.shared - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
-
- org.anchoranalysis.plugin.image.feature.bean.object.single.slice - package org.anchoranalysis.plugin.image.feature.bean.object.single.slice
-
Implementations of
FeatureSingleObject that processes an object
slice-by-slice in the z-dimension.
- org.anchoranalysis.plugin.image.feature.bean.object.single.surface - package org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
- org.anchoranalysis.plugin.image.feature.bean.physical - package org.anchoranalysis.plugin.image.feature.bean.physical
-
Beans involving physical units for measurement.
- org.anchoranalysis.plugin.image.feature.bean.score - package org.anchoranalysis.plugin.image.feature.bean.score
-
- org.anchoranalysis.plugin.image.feature.bean.shared - package org.anchoranalysis.plugin.image.feature.bean.shared
-
- org.anchoranalysis.plugin.image.feature.bean.shared.object - package org.anchoranalysis.plugin.image.feature.bean.shared.object
-
- org.anchoranalysis.plugin.image.feature.bean.stack.intensity - package org.anchoranalysis.plugin.image.feature.bean.stack.intensity
-
- org.anchoranalysis.plugin.image.feature.bean.stack.object - package org.anchoranalysis.plugin.image.feature.bean.stack.object
-
- org.anchoranalysis.plugin.image.feature.object - package org.anchoranalysis.plugin.image.feature.object
-
Non-bean classes that help calculate features from
ObjectMasks.
- org.anchoranalysis.plugin.image.feature.object.calculation.delegate - package org.anchoranalysis.plugin.image.feature.object.calculation.delegate
-
Implementations of
CalculationPart as used by
features elsewhere in this package.
- org.anchoranalysis.plugin.image.feature.object.calculation.single - package org.anchoranalysis.plugin.image.feature.object.calculation.single
-
- org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological - package org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
-
- org.anchoranalysis.plugin.image.feature.stack.calculation - package org.anchoranalysis.plugin.image.feature.stack.calculation
-
Implementations of
CalculationPart that process
Stacks as used by features elsewhere in this package.
- org.anchoranalysis.plugin.image.intensity - package org.anchoranalysis.plugin.image.intensity
-
Non-bean for operations or calculations relating to intensity.
- org.anchoranalysis.plugin.image.intensity.level - package org.anchoranalysis.plugin.image.intensity.level
-
Non-beans for calculating a thresholding level from itensity values.
- org.anchoranalysis.plugin.image.object - package org.anchoranalysis.plugin.image.object
-
- org.anchoranalysis.plugin.image.object.merge - package org.anchoranalysis.plugin.image.object.merge
-
- org.anchoranalysis.plugin.image.object.merge.condition - package org.anchoranalysis.plugin.image.object.merge.condition
-
- org.anchoranalysis.plugin.image.object.merge.priority - package org.anchoranalysis.plugin.image.object.merge.priority
-
- org.anchoranalysis.plugin.image.provider - package org.anchoranalysis.plugin.image.provider
-
Non-bean classes pertaining to
Providers.
- org.anchoranalysis.plugin.image.segment.thresholder.slice - package org.anchoranalysis.plugin.image.segment.thresholder.slice
-
Non-beans pertaining to segmenting a z-stack slice-by-slice.
- org.anchoranalysis.plugin.image.segment.watershed.encoding - package org.anchoranalysis.plugin.image.segment.watershed.encoding
-
Encoding voxels in a watershed-transformation implementation.
- org.anchoranalysis.plugin.image.task.bean - package org.anchoranalysis.plugin.image.task.bean
-
A parent package for many different kinds of tasks.
- org.anchoranalysis.plugin.image.task.bean.feature - package org.anchoranalysis.plugin.image.task.bean.feature
-
- org.anchoranalysis.plugin.image.task.bean.feature.source - package org.anchoranalysis.plugin.image.task.bean.feature.source
-
Source of rows in feature-tables with
FeatureSource and derived classes.
- org.anchoranalysis.plugin.image.task.bean.format - package org.anchoranalysis.plugin.image.task.bean.format
-
Tasks for converting image-formats.
- org.anchoranalysis.plugin.image.task.bean.format.convertstyle - package org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Different approaches for converting sets of channels (RGB, independently etc.) to another image
format.
- org.anchoranalysis.plugin.image.task.bean.grouped - package org.anchoranalysis.plugin.image.task.bean.grouped
-
Tasks that involved stacks (usually each channel from an image) that are somehow
grouped-together.
- org.anchoranalysis.plugin.image.task.bean.grouped.histogram - package org.anchoranalysis.plugin.image.task.bean.grouped.histogram
-
Task(s) to export histograms of intensity values.
- org.anchoranalysis.plugin.image.task.bean.grouped.raster - package org.anchoranalysis.plugin.image.task.bean.grouped.raster
-
Task(s) to calculate the mean of channels grouped together.
- org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels - package org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selecting a subset of a set of channels.
- org.anchoranalysis.plugin.image.task.bean.labeller - package org.anchoranalysis.plugin.image.task.bean.labeller
-
Associating labels with images.
- org.anchoranalysis.plugin.image.task.bean.scale - package org.anchoranalysis.plugin.image.task.bean.scale
-
Tasks to scale an image.
- org.anchoranalysis.plugin.image.task.bean.segment - package org.anchoranalysis.plugin.image.task.bean.segment
-
Tasks to segment an image.
- org.anchoranalysis.plugin.image.task.bean.slice - package org.anchoranalysis.plugin.image.task.bean.slice
-
Tasks that process on one or more slices from a z-stack.
- org.anchoranalysis.plugin.image.task.feature - package org.anchoranalysis.plugin.image.task.feature
-
Non-bean classes pertaining to
Features as used in tasks.
- org.anchoranalysis.plugin.image.task.feature.calculator - package org.anchoranalysis.plugin.image.task.feature.calculator
-
Non-beans for calculating
Features.
- org.anchoranalysis.plugin.image.task.grouped - package org.anchoranalysis.plugin.image.task.grouped
-
Non-bean classes about grouping channels or other inputs.
- org.anchoranalysis.plugin.image.task.labeller - package org.anchoranalysis.plugin.image.task.labeller
-
Non-bean classes about labelling images.
- org.anchoranalysis.plugin.image.task.segment - package org.anchoranalysis.plugin.image.task.segment
-
Non-bean classes for image-segmentation.
- org.anchoranalysis.plugin.image.task.stack - package org.anchoranalysis.plugin.image.task.stack
-
Non-bean classes pertaining to stacks and channels as used in tasks.
- org.anchoranalysis.plugin.image.thumbnail - package org.anchoranalysis.plugin.image.thumbnail
-
Non-bean classes for thumbnail creation.
- org.anchoranalysis.plugin.imagej.bean.channel.provider - package org.anchoranalysis.plugin.imagej.bean.channel.provider
-
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
-
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
-
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
-
- org.anchoranalysis.plugin.imagej.bean.define - package org.anchoranalysis.plugin.imagej.bean.define
-
- org.anchoranalysis.plugin.imagej.bean.mask.provider - package org.anchoranalysis.plugin.imagej.bean.mask.provider
-
- org.anchoranalysis.plugin.imagej.bean.object.provider - package org.anchoranalysis.plugin.imagej.bean.object.provider
-
- org.anchoranalysis.plugin.imagej.bean.object.segment - package org.anchoranalysis.plugin.imagej.bean.object.segment
-
- org.anchoranalysis.plugin.imagej.bean.stack.provider - package org.anchoranalysis.plugin.imagej.bean.stack.provider
-
- org.anchoranalysis.plugin.imagej.bean.threshold - package org.anchoranalysis.plugin.imagej.bean.threshold
-
- org.anchoranalysis.plugin.imagej.channel.provider - package org.anchoranalysis.plugin.imagej.channel.provider
-
- org.anchoranalysis.plugin.imagej.mask - package org.anchoranalysis.plugin.imagej.mask
-
- org.anchoranalysis.plugin.io.bean.channel.map - package org.anchoranalysis.plugin.io.bean.channel.map
-
- org.anchoranalysis.plugin.io.bean.file.copy.method - package org.anchoranalysis.plugin.io.bean.file.copy.method
-
Methods for copying files on the file-system.
- org.anchoranalysis.plugin.io.bean.file.copy.naming - package org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Rules for preserving or changing the naming of files when copying on the file-system.
- org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster - package org.anchoranalysis.plugin.io.bean.file.copy.naming.cluster
-
- org.anchoranalysis.plugin.io.bean.file.group - package org.anchoranalysis.plugin.io.bean.file.group
-
Grouping files together so that they collectively represent a single entity.
- org.anchoranalysis.plugin.io.bean.file.group.check - package org.anchoranalysis.plugin.io.bean.file.group.check
-
Tests that are applied when grouping files in org.anchoranalysis.plugin.io.bean.file.group
- org.anchoranalysis.plugin.io.bean.file.group.parser - package org.anchoranalysis.plugin.io.bean.file.group.parser
-
Parsing file-paths to determine file-grouping in org.anchoranalysis.plugin.io.bean.file.group
- org.anchoranalysis.plugin.io.bean.file.namer - package org.anchoranalysis.plugin.io.bean.file.namer
-
- org.anchoranalysis.plugin.io.bean.file.namer.patternspan - package org.anchoranalysis.plugin.io.bean.file.namer.patternspan
-
Implementations of
FileNamer that look for a
pattern across many files.
- org.anchoranalysis.plugin.io.bean.file.path - package org.anchoranalysis.plugin.io.bean.file.path
-
Beans to specify a file-path.
- org.anchoranalysis.plugin.io.bean.file.path.prefixer - package org.anchoranalysis.plugin.io.bean.file.path.prefixer
-
- org.anchoranalysis.plugin.io.bean.file.pattern - package org.anchoranalysis.plugin.io.bean.file.pattern
-
Extracting a pattern from a file-path.
- org.anchoranalysis.plugin.io.bean.file.provider - package org.anchoranalysis.plugin.io.bean.file.provider
-
- org.anchoranalysis.plugin.io.bean.input - package org.anchoranalysis.plugin.io.bean.input
-
- org.anchoranalysis.plugin.io.bean.input.channel - package org.anchoranalysis.plugin.io.bean.input.channel
-
- org.anchoranalysis.plugin.io.bean.input.files - package org.anchoranalysis.plugin.io.bean.input.files
-
- org.anchoranalysis.plugin.io.bean.input.files.provider - package org.anchoranalysis.plugin.io.bean.input.files.provider
-
- org.anchoranalysis.plugin.io.bean.input.filter - package org.anchoranalysis.plugin.io.bean.input.filter
-
- org.anchoranalysis.plugin.io.bean.input.manifest - package org.anchoranalysis.plugin.io.bean.input.manifest
-
- org.anchoranalysis.plugin.io.bean.input.stack - package org.anchoranalysis.plugin.io.bean.input.stack
-
- org.anchoranalysis.plugin.io.bean.metadata.header - package org.anchoranalysis.plugin.io.bean.metadata.header
-
Different types of image-file-formats whose headers can provide
ImageMetadata.
- org.anchoranalysis.plugin.io.bean.metadata.reader - package org.anchoranalysis.plugin.io.bean.metadata.reader
-
- org.anchoranalysis.plugin.io.bean.path.derive - package org.anchoranalysis.plugin.io.bean.path.derive
-
- org.anchoranalysis.plugin.io.bean.stack.reader - package org.anchoranalysis.plugin.io.bean.stack.reader
-
- org.anchoranalysis.plugin.io.bean.stack.writer - package org.anchoranalysis.plugin.io.bean.stack.writer
-
- org.anchoranalysis.plugin.io.bean.summarizer - package org.anchoranalysis.plugin.io.bean.summarizer
-
Summarizing a set of elements into a descriptive-string.
- org.anchoranalysis.plugin.io.bean.summarizer.image - package org.anchoranalysis.plugin.io.bean.summarizer.image
-
Implementations of
Summarizer that summarize
images.
- org.anchoranalysis.plugin.io.bean.summarizer.input - package org.anchoranalysis.plugin.io.bean.summarizer.input
-
- org.anchoranalysis.plugin.io.bean.summarizer.path - package org.anchoranalysis.plugin.io.bean.summarizer.path
-
- org.anchoranalysis.plugin.io.bean.task - package org.anchoranalysis.plugin.io.bean.task
-
Implementations of
Task related to file-system
I/O.
- org.anchoranalysis.plugin.io.file.copy - package org.anchoranalysis.plugin.io.file.copy
-
Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.file.copy.
- org.anchoranalysis.plugin.io.input.filter - package org.anchoranalysis.plugin.io.input.filter
-
Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.input.filter.
- org.anchoranalysis.plugin.io.input.path - package org.anchoranalysis.plugin.io.input.path
-
Non-bean classes to help in processing paths.
- org.anchoranalysis.plugin.io.manifest - package org.anchoranalysis.plugin.io.manifest
-
Non-bean classes to help tasks in org.anchoranalysis.plugin.io.bean.input.manifest.
- org.anchoranalysis.plugin.io.multifile - package org.anchoranalysis.plugin.io.multifile
-
Non-bean classes to help use multiple files to represent a single
Stack.
- org.anchoranalysis.plugin.io.multifile.buffer - package org.anchoranalysis.plugin.io.multifile.buffer
-
Buffers used in org.anchoranalysis.plugin.io.multifile.
- org.anchoranalysis.plugin.io.naming.interval - package org.anchoranalysis.plugin.io.naming.interval
-
How to write parts of a time-interval in a file-name.
- org.anchoranalysis.plugin.io.shared - package org.anchoranalysis.plugin.io.shared
-
Objects used in shared-state in
Tasks in this
plugin.
- org.anchoranalysis.plugin.io.xml - package org.anchoranalysis.plugin.io.xml
-
Reading and writing metadata XML.
- org.anchoranalysis.plugin.ml.bean.classifier - package org.anchoranalysis.plugin.ml.bean.classifier
-
Beans that perform classification in some way.
- org.anchoranalysis.plugin.ml.bean.cluster - package org.anchoranalysis.plugin.ml.bean.cluster
-
Beans that perform clustering in some way.
- org.anchoranalysis.plugin.mpp.bean.addcriteria - package org.anchoranalysis.plugin.mpp.bean.addcriteria
-
- org.anchoranalysis.plugin.mpp.bean.bound - package org.anchoranalysis.plugin.mpp.bean.bound
-
- org.anchoranalysis.plugin.mpp.bean.check - package org.anchoranalysis.plugin.mpp.bean.check
-
- org.anchoranalysis.plugin.mpp.bean.contour - package org.anchoranalysis.plugin.mpp.bean.contour
-
Retrieving the contour
outline pixels along the exterior
outer contour of an
ObjectMask.
- org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler - package org.anchoranalysis.plugin.mpp.bean.contour.visitscheduler
-
- org.anchoranalysis.plugin.mpp.bean.define - package org.anchoranalysis.plugin.mpp.bean.define
-
Beans related to
Define involving
Mark or related classes.
- org.anchoranalysis.plugin.mpp.bean.object.provider - package org.anchoranalysis.plugin.mpp.bean.object.provider
-
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
-
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.single - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
-
- org.anchoranalysis.plugin.mpp.bean.proposer.merge - package org.anchoranalysis.plugin.mpp.bean.proposer.merge
-
- org.anchoranalysis.plugin.mpp.bean.proposer.orientation - package org.anchoranalysis.plugin.mpp.bean.proposer.orientation
-
- org.anchoranalysis.plugin.mpp.bean.proposer.points - package org.anchoranalysis.plugin.mpp.bean.proposer.points
-
- org.anchoranalysis.plugin.mpp.bean.proposer.points.contour - package org.anchoranalysis.plugin.mpp.bean.proposer.points.contour
-
Finding a point on the external
outer contour of an
ObjectMask.
- org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation - package org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
-
- org.anchoranalysis.plugin.mpp.bean.proposer.position - package org.anchoranalysis.plugin.mpp.bean.proposer.position
-
- org.anchoranalysis.plugin.mpp.bean.proposer.radii - package org.anchoranalysis.plugin.mpp.bean.proposer.radii
-
- org.anchoranalysis.plugin.mpp.bean.proposer.scalar - package org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
- org.anchoranalysis.plugin.mpp.bean.proposer.split - package org.anchoranalysis.plugin.mpp.bean.proposer.split
-
- org.anchoranalysis.plugin.mpp.bean.provider.collection - package org.anchoranalysis.plugin.mpp.bean.provider.collection
-
- org.anchoranalysis.plugin.mpp.bean.provider.single - package org.anchoranalysis.plugin.mpp.bean.provider.single
-
- org.anchoranalysis.plugin.mpp.bean.region - package org.anchoranalysis.plugin.mpp.bean.region
-
- org.anchoranalysis.plugin.mpp.bean.segment.binary - package org.anchoranalysis.plugin.mpp.bean.segment.binary
-
- org.anchoranalysis.plugin.mpp.bean.stack.provider - package org.anchoranalysis.plugin.mpp.bean.stack.provider
-
- org.anchoranalysis.plugin.mpp.contour - package org.anchoranalysis.plugin.mpp.contour
-
Performs a walk on every voxel on the contour of an object-mask.
- org.anchoranalysis.plugin.mpp.contour.distance - package org.anchoranalysis.plugin.mpp.contour.distance
-
A list of visited pixels which forms one contiguous path where each voxel neighbors each other.
- org.anchoranalysis.plugin.mpp.contour.path - package org.anchoranalysis.plugin.mpp.contour.path
-
A set of contiguously neighboring points along the outline of an object.
- org.anchoranalysis.plugin.mpp.contour.path.merge - package org.anchoranalysis.plugin.mpp.contour.path.merge
-
- org.anchoranalysis.plugin.mpp.contour.path.merge.strategy - package org.anchoranalysis.plugin.mpp.contour.path.merge.strategy
-
- org.anchoranalysis.plugin.mpp.experiment.bean.convert - package org.anchoranalysis.plugin.mpp.experiment.bean.convert
-
- org.anchoranalysis.plugin.mpp.experiment.bean.define - package org.anchoranalysis.plugin.mpp.experiment.bean.define
-
- org.anchoranalysis.plugin.mpp.experiment.bean.feature.report - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
-
- org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
-
- org.anchoranalysis.plugin.mpp.experiment.bean.feature.source - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.source
-
- org.anchoranalysis.plugin.mpp.experiment.bean.objects - package org.anchoranalysis.plugin.mpp.experiment.bean.objects
-
- org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition - package org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
-
- org.anchoranalysis.plugin.mpp.experiment.bean.segment - package org.anchoranalysis.plugin.mpp.experiment.bean.segment
-
- org.anchoranalysis.plugin.mpp.experiment.objects - package org.anchoranalysis.plugin.mpp.experiment.objects
-
Non-bean classes used in org.anchoranalysis.plugin.mpp.experiment.bean.objects.
- org.anchoranalysis.plugin.mpp.experiment.objects.csv - package org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
Reading rows from a CSV file.
- org.anchoranalysis.plugin.mpp.experiment.shared - package org.anchoranalysis.plugin.mpp.experiment.shared
-
Shared-state use across tasks in this JAR.
- org.anchoranalysis.plugin.mpp.feature.bean.mark.collection - package org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
-
- org.anchoranalysis.plugin.mpp.feature.bean.mark.direction - package org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
-
- org.anchoranalysis.plugin.mpp.feature.bean.mark.radii - package org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
-
Implementations of
FeatureMark to measure or
calculate radii.
- org.anchoranalysis.plugin.mpp.feature.bean.mark.region - package org.anchoranalysis.plugin.mpp.feature.bean.mark.region
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.all - package org.anchoranalysis.plugin.mpp.feature.bean.memo.all
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.ind - package org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
-
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- org.anchoranalysis.plugin.mpp.feature.bean.unit - package org.anchoranalysis.plugin.mpp.feature.bean.unit
-
Beans to convert between units.
- org.anchoranalysis.plugin.mpp.feature.overlap - package org.anchoranalysis.plugin.mpp.feature.overlap
-
Implementations of
CalculationPart to calculate
overlap between two entities.
- org.anchoranalysis.plugin.mpp.segment.bean.annealing - package org.anchoranalysis.plugin.mpp.segment.bean.annealing
-
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
-
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
-
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.voxelized - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.voxelized
-
Implementations of
KernelBirth that are
independent but use the voxelized state of a
Mark.
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks - package org.anchoranalysis.plugin.mpp.segment.bean.marks
-
Beans to perform segmentation involving
Marks and related
classes.
- org.anchoranalysis.plugin.mpp.segment.bean.marks.dual - package org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks.partition - package org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized - package org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
-
- org.anchoranalysis.plugin.mpp.segment.bean.marks.weight - package org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
-
Deriving a weight for a
Mark.
- org.anchoranalysis.plugin.mpp.segment.bean.optimization - package org.anchoranalysis.plugin.mpp.segment.bean.optimization
-
Beans related to performing optimization with marked-point-processes.
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
-
- org.anchoranalysis.plugin.mpp.segment.kernel.assigner - package org.anchoranalysis.plugin.mpp.segment.kernel.assigner
-
- org.anchoranalysis.plugin.mpp.segment.kernel.updater - package org.anchoranalysis.plugin.mpp.segment.kernel.updater
-
- org.anchoranalysis.plugin.mpp.segment.optimization - package org.anchoranalysis.plugin.mpp.segment.optimization
-
Non-bean classes to help with optimization in org.anchoranalysis.plugin.mpp.segment.bean.optimization and sub-packages.
- org.anchoranalysis.plugin.mpp.segment.shared - package org.anchoranalysis.plugin.mpp.segment.shared
-
Stared-state for segmentation tasks involving mark-point-processes.
- org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn - package org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.maskrcnn
-
Decodes the outputted tensors from a
Mask
R-CNN implementation.
- org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text - package org.anchoranalysis.plugin.onnx.bean.object.segment.decode.instance.text
-
- org.anchoranalysis.plugin.onnx.bean.object.segment.stack - package org.anchoranalysis.plugin.onnx.bean.object.segment.stack
-
- org.anchoranalysis.plugin.onnx.model - package org.anchoranalysis.plugin.onnx.model
-
- org.anchoranalysis.plugin.opencv - package org.anchoranalysis.plugin.opencv
-
- org.anchoranalysis.plugin.opencv.bean.color - package org.anchoranalysis.plugin.opencv.bean.color
-
Operations involving color-spaces and
OpenCV.
- org.anchoranalysis.plugin.opencv.bean.feature - package org.anchoranalysis.plugin.opencv.bean.feature
-
Extracting features using
OpenCV.
- org.anchoranalysis.plugin.opencv.bean.interpolate - package org.anchoranalysis.plugin.opencv.bean.interpolate
-
Interpolation beans that use OpenCV.
- org.anchoranalysis.plugin.opencv.bean.object.segment.stack - package org.anchoranalysis.plugin.opencv.bean.object.segment.stack
-
Segmentation of a
Stack using OpenCV.
- org.anchoranalysis.plugin.opencv.bean.stack - package org.anchoranalysis.plugin.opencv.bean.stack
-
- org.anchoranalysis.plugin.opencv.convert - package org.anchoranalysis.plugin.opencv.convert
-
Conversion to/from
OpenCV data-structures.
- org.anchoranalysis.plugin.opencv.interpolator - package org.anchoranalysis.plugin.opencv.interpolator
-
Interpolation non-beans that use OpenCV.
- org.anchoranalysis.plugin.opencv.segment - package org.anchoranalysis.plugin.opencv.segment
-
Non-bean classes pertaining to segmentation.
- org.anchoranalysis.plugin.operator.feature.bean - package org.anchoranalysis.plugin.operator.feature.bean
-
Features that combine or convert other features in a generic way.
- org.anchoranalysis.plugin.operator.feature.bean.arithmetic - package org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
Arithmetic involving features.
- org.anchoranalysis.plugin.operator.feature.bean.conditional - package org.anchoranalysis.plugin.operator.feature.bean.conditional
-
Conditional operations involving features.
- org.anchoranalysis.plugin.operator.feature.bean.list - package org.anchoranalysis.plugin.operator.feature.bean.list
-
Operations that extract a single value from a list of features.
- org.anchoranalysis.plugin.operator.feature.bean.range - package org.anchoranalysis.plugin.operator.feature.bean.range
-
Features that compare against a range of values.
- org.anchoranalysis.plugin.operator.feature.bean.replace - package org.anchoranalysis.plugin.operator.feature.bean.replace
-
Replaces particular values if they are returned from a feature.
- org.anchoranalysis.plugin.operator.feature.bean.statistics - package org.anchoranalysis.plugin.operator.feature.bean.statistics
-
Converts feature values based upon a statistical measure of distribution.
- org.anchoranalysis.plugin.operator.feature.physical - package org.anchoranalysis.plugin.operator.feature.physical
-
Converting to/from physical units.
- org.anchoranalysis.plugin.operator.feature.statistics - package org.anchoranalysis.plugin.operator.feature.statistics
-
Non-bean statistical operations.
- org.anchoranalysis.plugin.points.bean - package org.anchoranalysis.plugin.points.bean
-
Beans that fit or otherwise manipulate sets of points.
- org.anchoranalysis.plugin.points.bean.convexhull - package org.anchoranalysis.plugin.points.bean.convexhull
-
Convex hull operations.
- org.anchoranalysis.plugin.points.bean.feature - package org.anchoranalysis.plugin.points.bean.feature
-
Features related to points and fitting points to conics.
- org.anchoranalysis.plugin.points.bean.fitter - package org.anchoranalysis.plugin.points.bean.fitter
-
Fitting geometric structures to points.
- org.anchoranalysis.plugin.points.calculate.ellipse - package org.anchoranalysis.plugin.points.calculate.ellipse
-
- org.anchoranalysis.plugin.points.calculate.ellipsoid - package org.anchoranalysis.plugin.points.calculate.ellipsoid
-
- org.anchoranalysis.plugin.points.convexhull - package org.anchoranalysis.plugin.points.convexhull
-
Non-bean convex hull operations.
- org.anchoranalysis.plugin.quick.bean.experiment - package org.anchoranalysis.plugin.quick.bean.experiment
-
Quickly defining experiments via several assumptions, including particular file-paths.
- org.anchoranalysis.plugin.quick.bean.file.path.derive - package org.anchoranalysis.plugin.quick.bean.file.path.derive
-
Deriving paths from existing paths as helpful to quickly defined experiments.
- org.anchoranalysis.plugin.quick.bean.input - package org.anchoranalysis.plugin.quick.bean.input
-
Specifying inputs when quickly defining an experiment.
- org.anchoranalysis.plugin.quick.bean.input.filepathappend - package org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
Appending other entities to inputs when quickly defining experiments.
- org.anchoranalysis.plugin.quick.bean.structure - package org.anchoranalysis.plugin.quick.bean.structure
-
Specifying a structure of subdirectories and filenames when quickly defining an experiment.
- org.anchoranalysis.spatial.axis - package org.anchoranalysis.spatial.axis
-
Identifying the three standard axes in 3D cartesian coordinates.
- org.anchoranalysis.spatial.box - package org.anchoranalysis.spatial.box
-
Axis-aligned bounding-boxes and related operations.
- org.anchoranalysis.spatial.orientation - package org.anchoranalysis.spatial.orientation
-
Various methods to specify the orientation (general direction) of an entity.
- org.anchoranalysis.spatial.point - package org.anchoranalysis.spatial.point
-
A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
- org.anchoranalysis.spatial.point.consumer - package org.anchoranalysis.spatial.point.consumer
-
Functional interfaces that accept cartesian coordinate points specified in different ways.
- org.anchoranalysis.spatial.rtree - package org.anchoranalysis.spatial.rtree
-
R-Tree data structure and related operations.
- org.anchoranalysis.spatial.scale - package org.anchoranalysis.spatial.scale
-
How to much to scale an entity in Cartesian space by.
- org.anchoranalysis.test - package org.anchoranalysis.test
-
Testing utilities and fixtures with no greater downstream dependency than anchor-core.
- org.anchoranalysis.test.experiment - package org.anchoranalysis.test.experiment
-
Testing utilities and fixtures with no greater downstream dependency than
anchor-experiment or anchor-mpp or anchor-mpp-io.
- org.anchoranalysis.test.experiment.launcher - package org.anchoranalysis.test.experiment.launcher
-
Launches an anchor binary from a shell and runs an experiment.
- org.anchoranalysis.test.experiment.task - package org.anchoranalysis.test.experiment.task
-
Helper classes to execute
Tasks in tests.
- org.anchoranalysis.test.feature - package org.anchoranalysis.test.feature
-
Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
- org.anchoranalysis.test.feature.plugins - package org.anchoranalysis.test.feature.plugins
-
Testing utilities and fixtures with no greater downstream dependency than
anchor-image-feature or anchor-mpp.
- org.anchoranalysis.test.feature.plugins.mockfeature - package org.anchoranalysis.test.feature.plugins.mockfeature
-
A mocked feature internally using a feature-calculation.
- org.anchoranalysis.test.feature.plugins.objects - package org.anchoranalysis.test.feature.plugins.objects
-
Fixtures for creating object-masks and related feature-inputs.
- Orientation - Class in org.anchoranalysis.image.io.bean.object.draw
-
Writes a line through the midpoint illustrating the orientation of the object
- Orientation() - Constructor for class Orientation
-
- Orientation - Class in org.anchoranalysis.spatial.orientation
-
The
orientation (direction) in
2D or 3D Euclidean space.
- Orientation() - Constructor for class Orientation
-
- Orientation2D - Class in org.anchoranalysis.spatial.orientation
-
A simple angular orientation the 2D plane, relative to the x-axis.
- Orientation2D(double) - Constructor for class Orientation2D
-
- Orientation2D() - Constructor for class Orientation2D
-
- Orientation3DEulerAngles - Class in org.anchoranalysis.spatial.orientation
-
An orientation using three angle parameters for the rotation.
- Orientation3DEulerAngles(double, double, double) - Constructor for class Orientation3DEulerAngles
-
- OrientationAndRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
Proposes both an orientation and radii for a
ConicBase
- OrientationAndRadiiProposer(RadiiProposer, OrientationProposer) - Constructor for class OrientationAndRadiiProposer
-
- OrientationAxisAngle - Class in org.anchoranalysis.spatial.orientation
-
An orientation in axis-angle representation.
- OrientationAxisAngle(Vector3d, double) - Constructor for class OrientationAxisAngle
-
- OrientationChange - Enum in org.anchoranalysis.image.core.dimensions
-
Changes orientation of an image in the XY plane.
- OrientationProposer - Class in org.anchoranalysis.mpp.bean.proposer
-
- OrientationProposer() - Constructor for class OrientationProposer
-
- OrientationReader - Class in org.anchoranalysis.io.bioformats.metadata
-
Reads the image-orientation from EXIF metadata, if specified in an image-file.
- OrientationRotationMatrix - Class in org.anchoranalysis.spatial.orientation
-
Orients an object by rotating anti-clockwise with an explicit
RotationMatrix.
- OrientationRotationMatrix() - Constructor for class OrientationRotationMatrix
-
- OrientationRotationMatrix(RotationMatrix) - Constructor for class OrientationRotationMatrix
-
- otherVertex(V) - Method in class TypedEdge
-
The other vertex on the edge
- Otsu - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Performs auto-thresholding using Otsu's method.
- Otsu() - Constructor for class Otsu
-
- OtsuWeighted - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Similar to Otsu, but weighs the variances differently of background and foreground.
- OtsuWeighted() - Constructor for class OtsuWeighted
-
- OtsuWeighted(double, double) - Constructor for class OtsuWeighted
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixer
-
Provides a prefix which can be prepended to all output files.
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class HomeSubdirectory
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class Rooted
-
- outFilePrefix(NamedPath, Optional<String>, PathPrefixerContext) - Method in class ExperimentStructure
-
- outFilePrefixAvoidResolve(NamedPath, Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
-
Provides a prefix which can be prepended to all output files.
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class IncrementingNumber
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
-
Determines the out-file prefix from a path
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class DirectoryStructure
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class FromDescriptiveName
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class IfIncrementingNumberRequested
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class LastDirectoryAsPrefix
-
- outFilePrefixFromPath(NamedPath, Path, PathPrefixerContext) - Method in class PathRegEx
-
- outgoingEdgesFor(V) - Method in class GraphWithPayload
-
All outgoing edges for a given vertex.
- Outline - Class in org.anchoranalysis.image.io.bean.object.draw
-
Draws the outline of each object-mask.
- Outline() - Constructor for class Outline
-
- Outline(int) - Constructor for class Outline
-
- Outline(int, boolean) - Constructor for class Outline
-
- OutlineKernel - Class in org.anchoranalysis.image.voxel.kernel.outline
-
Sets voxels on the outline of an object to be on and otherwise off.
- OutlineKernel() - Constructor for class OutlineKernel
-
- OutlineKernelBase - Class in org.anchoranalysis.image.voxel.kernel.outline
-
A base class for kernels that find the outline of an
ObjectMask.
- OutlineKernelBase() - Constructor for class OutlineKernelBase
-
Default constructor.
- OutlineKernelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
-
- OutlineKernelBase() - Constructor for class OutlineKernelBase
-
- OutlineKernelNeighborMatchValue - Class in org.anchoranalysis.image.voxel.kernel.outline
-
Outputs the outline of an object-mask, but only for voxels on the exterior which neighbor a
binary-mask.
- OutlineKernelNeighborMatchValue(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class OutlineKernelNeighborMatchValue
-
Creates for an object.
- OutlinePreserveRelativeSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object
-
Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it
centered in a window of a certain size.
- OutlinePreserveRelativeSize() - Constructor for class OutlinePreserveRelativeSize
-
- outlineSingleColor(int, DisplayStack, RGBColor) - Static method in class DrawObjectsGenerator
-
A generator that draws an outline around objects on a background using a single color for all
objects.
- outlineVariedColors(int, int, DisplayStack) - Static method in class DrawObjectsGenerator
-
A generator that draws an outline around objects on a background using varied colors for the
objects.
- outlineVariedColors(int, int, Either<Dimensions, DisplayStack>) - Static method in class DrawObjectsGenerator
-
A generator that draws an outline around objects on a background using varied colors for the
objects.
- outlineWithColorIndex(int, ColorIndex) - Static method in class DrawObjectsGenerator
-
A generator that draws an outline around objects using a particular color-index.
- output() - Method in class ExecutionArguments
-
Arguments to help specify the outputs from the experiment.
- output(InputOutputContext) - Method in class OutputFeatureTable
-
Outputs the feature-table.
- output(NamedProvider<Stack>, String, boolean, OutputterChecked) - Static method in class NamedStacksOutputter
-
Writes all or a subset from a set of named-stacks to a directory as a raster.
- output(String, boolean) - Method in class NamedProviderOutputter
-
Outputs the entities using a particular output-name.
- OUTPUT_BY_GROUP - Static variable in class CompareAnnotations
-
- OUTPUT_DEFAULT_NON_AGGREGATED - Static variable in class FeatureOutputNames
-
If not otherwise specified, the output name for a non-aggregated CSV of the results.
- OUTPUT_ENERGY_STACK_DIRECTORY - Static variable in class EnergyStackWriter
-
- OUTPUT_EXECUTION_TIME - Static variable in class OutputExperiment
-
- OUTPUT_FEATURE_TABLE - Static variable in class OutputFeatureTable
-
- OUTPUT_MANIFEST - Static variable in class OutputExperiment
-
- OUTPUT_MANIFEST - Static variable in class Task
-
- OUTPUT_RESULTS - Static variable in class ExportFeatures
-
- OUTPUT_SUFFIX_AGGREGATED - Static variable in class FeatureOutputNames
-
- OUTPUT_SUFFIX_AGGREGATED_GROUP - Static variable in class FeatureOutputNames
-
- OUTPUT_SUFFIX_GROUP - Static variable in class FeatureOutputNames
-
- OUTPUT_THUMBNAILS - Static variable in class FeatureExporter
-
The output-name for writing thumbnails.
- outputAfterAllTasksAreExecuted(Outputter) - Method in interface ExperimentState
-
- outputAfterAllTasksAreExecuted(Outputter) - Method in class SegmentMarksState
-
- OutputArguments - Class in org.anchoranalysis.experiment.arguments
-
Arguments that can further specify an experiment's output in addition to its bean
specification.
- OutputArguments() - Constructor for class OutputArguments
-
- outputBeforeAnyTasksAreExecuted(Outputter) - Method in interface ExperimentState
-
- outputBeforeAnyTasksAreExecuted(Outputter) - Method in class SegmentMarksState
-
- OutputDirectoryAlreadyExistsException - Exception in org.anchoranalysis.io.output.error
-
When an output-directory already exists.
- OutputDirectoryAlreadyExistsException(String) - Constructor for exception OutputDirectoryAlreadyExistsException
-
- OutputEnabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Whether a particular output, identified by a textual name, is enabled or not.
- OutputEnabled() - Constructor for class OutputEnabled
-
- OutputEnabledDelta - Class in org.anchoranalysis.io.output.recorded
-
Additional output-names to enable or disable from an existing set of output-enabled rules.
- OutputEnabledDelta() - Constructor for class OutputEnabledDelta
-
- OutputEnabledMutable - Class in org.anchoranalysis.io.output.enabled
-
A specific set of first-level outputs are enabled, to which more can be added.
- OutputEnabledMutable(String...) - Constructor for class OutputEnabledMutable
-
Creates with one or more enabled outputs.
- OutputEnabledMutable(SingleLevelOutputEnabled, String...) - Constructor for class OutputEnabledMutable
-
Creates with one or more enabled outputs.
- OutputEnabledRules - Class in org.anchoranalysis.io.output.bean.rules
-
- OutputEnabledRules() - Constructor for class OutputEnabledRules
-
- OutputEnableRulesSpecify - Class in org.anchoranalysis.io.output.bean.rules
-
Base class for an
OutputEnabledRules that specifies particular output-names for first and
second levels.
- OutputEnableRulesSpecify(StringSet) - Constructor for class OutputEnableRulesSpecify
-
Create with a specific set of first-level output names.
- OutputEnableRulesSpecify() - Constructor for class OutputEnableRulesSpecify
-
- OutputExperiment - Class in org.anchoranalysis.experiment.bean.io
-
An experiment that uses a
OutputManager to specify the outputting of results.
- OutputExperiment() - Constructor for class OutputExperiment
-
- OutputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path
-
SelectParam<Path> factory for outputs.
- OutputFeatureTable - Class in org.anchoranalysis.image.io.bean.object.feature
-
Specifies a table of feature-calculations on objects.
- OutputFeatureTable() - Constructor for class OutputFeatureTable
-
- outputFormatString() - Method in class IndexableOutputNameStyle
-
- outputFormatString() - Method in class IntegerSuffixOutputNameStyle
-
- outputFormatString() - Method in class StringSuffixOutputNameStyle
-
- outputGroupedData(ConsistentChannelChecker, InputOutputContext) - Method in class GroupMapByName
-
Outputs the "grouped" data to the filesystem
- outputHeaderToWriter(PrintWriter, String) - Method in class AggIDCounter
-
- outputHeaderToWriter(PrintWriter) - Method in class Aggregator
-
- OutputManager - Class in org.anchoranalysis.io.output.bean
-
Responsible for making decisions on where output goes and what form it takes.
- OutputManager() - Constructor for class OutputManager
-
- outputName(String) - Static method in class FileMatch
-
Match a file whose output-name matches a specific value.
- outputNameForGroups() - Method in class GroupedStackBase
-
The first-level output-name used for determining if groups are written.
- outputNameForGroups() - Method in class ExportImageHistograms
-
- outputNameForGroups() - Method in class GroupedMeanChannelTask
-
- outputNames() - Method in class FeatureOutputMetadata
-
- OutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
- OutputNameStyle(String) - Constructor for class OutputNameStyle
-
- OutputNameStyle() - Constructor for class OutputNameStyle
-
- OutputPattern - Class in org.anchoranalysis.io.generator.sequence.pattern
-
A particular naming pattern files follow when outputted.
- OutputPattern(Optional<String>, IndexableOutputNameStyle, boolean, Optional<ManifestDescription>) - Constructor for class OutputPattern
-
- OutputPatternIntegerSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern
-
A
OutputPattern that outputs a file-name with a trailing integer index.
- OutputPatternIntegerSuffix(String, boolean) - Constructor for class OutputPatternIntegerSuffix
-
Creates in a subdirectory, using the outputName as both the subdirectory name and the prefix.
- OutputPatternIntegerSuffix(String, String) - Constructor for class OutputPatternIntegerSuffix
-
Creates in a subdirectory, using the output-name as the subdirectory name, and a specific
prefix.
- OutputPatternIntegerSuffix(String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix
-
- OutputPatternIntegerSuffix(String, String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix
-
- OutputPatternIntegerSuffix(String, boolean, String, int, boolean, Optional<ManifestDescription>) - Constructor for class OutputPatternIntegerSuffix
-
Creates with a full set of flexibility about how the filename appears and whether a
subdirectory is used.
- OutputPatternStringSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern
-
A
OutputPattern that outputs a file-name with a trailing string index.
- OutputPatternStringSuffix(String, boolean) - Constructor for class OutputPatternStringSuffix
-
Creates without a prefix.
- OutputPatternStringSuffix(String, boolean, String) - Constructor for class OutputPatternStringSuffix
-
Creates with a prefix.
- OutputPrefixerSettings - Class in org.anchoranalysis.io.output.path.prefixer
-
Arguments influencing into which directory outputs are written, and how identifiers are
expressed.
- OutputPrefixerSettings() - Constructor for class OutputPrefixerSettings
-
- OutputPrefixWithExtension - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Copies files using whatever prefix is assigned to an input by the
OutputManager as the
file-name, adding the same extension as the source file.
- OutputPrefixWithExtension() - Constructor for class OutputPrefixWithExtension
-
- outputSelectParam(CommandLine) - Static method in class SelectParamFactory
-
Can point to either:
a path ending in .xml, assumed to BeanXML for an output manager
a directory, set as the outputDirectory in the input-context
- outputsEnabled() - Method in class Outputter
-
- OutputSequence - Interface in org.anchoranalysis.io.generator.sequence
-
A sequence of elements that are written to the same directory.
- OutputSequenceFactory<T> - Class in org.anchoranalysis.io.generator.sequence
-
Creates and starts a
OutputSequence with a particular generator and context.
- OutputSequenceFactory(Generator<T>, OutputterChecked) - Constructor for class OutputSequenceFactory
-
- OutputSequenceIncrementing<T> - Class in org.anchoranalysis.io.generator.sequence
-
A sequence of outputs that use the same generator, where each output increments an index by one
in the filename.
- OutputSequenceIncrementing(BoundOutputter<T>, int) - Constructor for class OutputSequenceIncrementing
-
- OutputSequenceIndexed<T,S> - Class in org.anchoranalysis.io.generator.sequence
-
A sequence of outputs that use the same generator with non-incrementing indexes for each output.
- OutputSequenceStackFactory - Class in org.anchoranalysis.image.io.stack.output
-
Creates
OutputSequence of different kinds for writing stacks to a directory.
- outputSharedObjects(SharedObjects, Optional<EnergyStack>, Outputter) - Method in class DefineOutputter
-
- OutputtedFile - Class in org.anchoranalysis.io.manifest.file
-
An entry in a
Manifest for an outputted file from an experiment.
- OutputtedFile(MutableDirectory, String, String, String, Optional<ManifestDescription>) - Constructor for class OutputtedFile
-
- OutputtedFile(MutableDirectory, String, String, String, ManifestDescription) - Constructor for class OutputtedFile
-
- Outputter - Class in org.anchoranalysis.io.output.outputter
-
- Outputter(OutputterChecked, ErrorReporter) - Constructor for class Outputter
-
- OutputterChecked - Class in org.anchoranalysis.io.output.outputter
-
A particular directory on the filesystem in which outputting can occur.
- OutputterDirectories - Class in org.anchoranalysis.mpp.segment.define
-
Directories into which collections of different types of objects are written to in a
define experiment
- OutputterTarget - Class in org.anchoranalysis.io.output.outputter.directory
-
The directory and prefix an outputter writes to.
- OutputterTarget(DirectoryWithPrefix, boolean) - Constructor for class OutputterTarget
-
- outputToWriter(PrintWriter) - Method in class AggIDCounter
-
- outputToWriter(PrintWriter) - Method in class Aggregator
-
- OutputWriteContext - Class in org.anchoranalysis.io.output.outputter
-
Settings and user-arguments for writing files.
- OutputWriteContext() - Constructor for class OutputWriteContext
-
Create with default state, including no default beans assigned.
- OutputWriteContext(OutputWriteSettings) - Constructor for class OutputWriteContext
-
- OutputWriteContext(OutputWriteSettings, Optional<ImageFileFormat>, ExecutionTimeRecorder) - Constructor for class OutputWriteContext
-
- OutputWriteFailedException - Exception in org.anchoranalysis.io.output.error
-
- OutputWriteFailedException(String) - Constructor for exception OutputWriteFailedException
-
- OutputWriteFailedException(String, HasFriendlyErrorMessage) - Constructor for exception OutputWriteFailedException
-
- OutputWriteFailedException(String, AnchorCombinableException) - Constructor for exception OutputWriteFailedException
-
- OutputWriteFailedException(Throwable) - Constructor for exception OutputWriteFailedException
-
- OutputWriteSettings - Class in org.anchoranalysis.io.output.bean
-
Settings for how to write output, including default writers.
- OutputWriteSettings() - Constructor for class OutputWriteSettings
-
- OutsideKernelPolicy - Enum in org.anchoranalysis.image.voxel.kernel
-
How to handle voxels whose neighbors are outside the scene.
- OutsideRange - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- OutsideRange() - Constructor for class OutsideRange
-
- overAll(Kernel, BinaryVoxels<UnsignedByteBuffer>, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateKernelHelper
-
Iterates over all voxels.
- overBox(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, ProcessKernelPointCursor) - Static method in class IterateKernelHelper
-
Iterates over only voxels contained within a bounding-box.
- overBoxUntil(Kernel, BinaryVoxels<UnsignedByteBuffer>, BoundingBox, KernelApplicationParameters, PredicateKernelPointCursor) - Static method in class IterateKernelHelper
-
Iterates over only voxels contained within a bounding-box until a predicate is matched
on a voxel.
- OverlapMaskBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapMaskBase() - Constructor for class OverlapMaskBase
-
- OverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapMIPBase() - Constructor for class OverlapMIPBase
-
- OverlapNumberVoxelsMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapNumberVoxelsMask() - Constructor for class OverlapNumberVoxelsMask
-
- OverlapNumVoxels - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapNumVoxels() - Constructor for class OverlapNumVoxels
-
- overlappingNumVoxels(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class FeaturePairMemoSingleRegion
-
- overlappingNumVoxels(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapMaskBase
-
- overlappingNumVoxels(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapMIPBase
-
- OverlappingObject<T> - Class in org.anchoranalysis.image.core.object.label
-
An object-mask that is founded to overlap with another during labelling.
- OverlappingObject(T, ObjectMask) - Constructor for class OverlappingObject
-
- OverlappingObjects - Class in org.anchoranalysis.annotation.io.assignment
-
- OverlappingObjects() - Constructor for class OverlappingObjects
-
- OverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapRatio() - Constructor for class OverlapRatio
-
- OverlapRatioMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
-
- OverlapRatioMask() - Constructor for class OverlapRatioMask
-
- OverlapRelative - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
Expresses the number of intersecting pixels between two objects as a ratio to something else
(denominator)
- OverlapRelative() - Constructor for class OverlapRelative
-
- OverlapRelativeToFirst - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
- OverlapRelativeToFirst() - Constructor for class OverlapRelativeToFirst
-
- OverlapRelativeToMaxVolume - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
Overlap ratio to the maximum number of pixels
- OverlapRelativeToMaxVolume() - Constructor for class OverlapRelativeToMaxVolume
-
- OverlapRelativeToMerged - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
- OverlapRelativeToMerged() - Constructor for class OverlapRelativeToMerged
-
- OverlapRelativeToSecond - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
- OverlapRelativeToSecond() - Constructor for class OverlapRelativeToSecond
-
- OverlapUtilities - Class in org.anchoranalysis.mpp.overlap
-
- overlapWith(VoxelizedMarkMemo, VoxelizedMarkMemo, int) - Static method in class OverlapUtilities
-
- overlapWithGlobalMask(FeatureCalculationInput<FeatureInputPairMemo>) - Method in class OverlapMaskBase
-
- overlapWithMaskGlobal(VoxelizedMarkMemo, VoxelizedMarkMemo, int, Voxels<UnsignedByteBuffer>, byte) - Static method in class OverlapUtilities
-
- Overlay - Class in org.anchoranalysis.image.bean.spatial.arrange
-
Overlays one image on the other.
- Overlay() - Constructor for class Overlay
-
- Overlay(String, String, String) - Constructor for class Overlay
-
- Overlay - Class in org.anchoranalysis.overlay
-
An entity that will eventually be drawn on top of an image.
- Overlay() - Constructor for class Overlay
-
- OverlayCollection - Class in org.anchoranalysis.overlay.collection
-
- OverlayCollection() - Constructor for class OverlayCollection
-
- OverlayCollection(Stream<Overlay>) - Constructor for class OverlayCollection
-
- OverlayCollectionMarkFactory - Class in org.anchoranalysis.mpp.overlay
-
Two-way factory.
- OverlayCollectionObjectFactory - Class in org.anchoranalysis.overlay.collection
-
Two-way factory.
- OverlayMark - Class in org.anchoranalysis.mpp.overlay
-
- OverlayMark(Mark, RegionMembershipWithFlags) - Constructor for class OverlayMark
-
- OverlayObjectMask - Class in org.anchoranalysis.overlay.object
-
- OverlayObjectMask(ObjectMask, int) - Constructor for class OverlayObjectMask
-
- OverlayProperties - Class in org.anchoranalysis.overlay
-
- OverlayProperties() - Constructor for class OverlayProperties
-
- RadiiMinRatio - Class in org.anchoranalysis.plugin.mpp.bean.check
-
- RadiiMinRatio() - Constructor for class RadiiMinRatio
-
- radiiOrdered() - Method in class ConicBase
-
- radiiOrderedResolved(Optional<Resolution>) - Method in class ConicBase
-
- RadiiProposer - Class in org.anchoranalysis.mpp.bean.proposer
-
- RadiiProposer() - Constructor for class RadiiProposer
-
- RadiiProposerRepeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.radii
-
- RadiiProposerRepeat() - Constructor for class RadiiProposerRepeat
-
- RadiiRandomizer - Class in org.anchoranalysis.mpp.mark.conic
-
Utility functions for generating random radii for
ConicBase
- RadiiRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
-
- RadiiRatio() - Constructor for class RadiiRatio
-
- radiusForRegion(int) - Method in class MarkWithPositionAndSingleRadius
-
- radiusForRegionSquared(int) - Method in class MarkWithPositionAndSingleRadius
-
- RandomCollection<T> - Class in org.anchoranalysis.mpp.pair
-
A collection of items from which one can randomly sample
- RandomCollection() - Constructor for class RandomCollection
-
- RandomCollectionWithAddCriteria<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
-
- RandomCollectionWithAddCriteria(Class<?>) - Constructor for class RandomCollectionWithAddCriteria
-
- randomIndex(RandomNumberGenerator) - Method in class MarkCollection
-
- randomizeRadii(Bound, RandomNumberGenerator, Optional<Resolution>, boolean) - Static method in class RadiiRandomizer
-
- randomMark(RandomNumberGenerator) - Method in class MarkCollection
-
- RandomNumberGenerator - Interface in org.anchoranalysis.core.random
-
Generates random numbers from various distributions.
- RandomNumberGeneratorBean - Class in org.anchoranalysis.bean.shared.random
-
- RandomNumberGeneratorBean() - Constructor for class RandomNumberGeneratorBean
-
- RandomNumberGeneratorMersenne - Class in org.anchoranalysis.core.random
-
Implements a random-number generator using the MersenneTwister algorithm.
- RandomNumberGeneratorMersenne(boolean) - Constructor for class RandomNumberGeneratorMersenne
-
Creates indicating whether to use a fixed-seed or not.
- RandomOrder - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- RandomOrder() - Constructor for class RandomOrder
-
- randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class BoundRotation
-
- randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class BoundRotation2D
-
- randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class BoundRotation3D
-
- RandomOrientation - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
-
- RandomOrientation() - Constructor for class RandomOrientation
-
- RandomOrientation(BoundRotation) - Constructor for class RandomOrientation
-
- RandomXY - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
-
- RandomXY() - Constructor for class RandomXY
-
- randOpen(RandomNumberGenerator) - Method in class ResolvedBound
-
A random value between the bounds (open interval)
- Range - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
The range (difference in values) between two quantiles
- Range() - Constructor for class Range
-
- Range<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
The statistical range between two values i.e.
- Range() - Constructor for class Range
-
- rangeChannelNum() - Method in class ParsedFilePathBag
-
- RangeCompareBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
- RangeCompareBase() - Constructor for class RangeCompareBase
-
- RangeCompareFromScalars<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
A base-class for setting the boundaries of the range using constant scalars
- RangeCompareFromScalars() - Constructor for class RangeCompareFromScalars
-
- rangeCPresent() - Method in class SizeExtents
-
- rangeLimitsIfEmpty(DefaultCategoryDataset) - Method in class BarPlot
-
- rangeLimitsIfEmpty(DefaultBoxAndWhiskerCategoryDataset) - Method in class BoxPlot
-
- rangeLimitsIfEmpty(XYDataset) - Method in class LinePlot
-
- rangeLimitsIfEmpty(S) - Method in class PlotIndexBase
-
- rangeSliceNum() - Method in class ParsedFilePathBag
-
- rangeTimeIndex() - Method in class ParsedFilePathBag
-
- rangeTPresent() - Method in class SizeExtents
-
- RasterArranger - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
- RasterArranger() - Constructor for class RasterArranger
-
- RasterDirectoryObjectsGenerator - Class in org.anchoranalysis.image.io.object.output.mask
-
Writes each object as a binary
Mask in a directory.
- RasterGenerator<T> - Class in org.anchoranalysis.image.io.stack.output.generator
-
Transfroms an entity to a
Stack and writes it to the file-system.
- RasterGenerator() - Constructor for class RasterGenerator
-
- RasterGeneratorBridge<T,V> - Class in org.anchoranalysis.image.io.stack.output.generator
-
Allows us to call an RasterGenerator<S> as if it was an RasterGenerator<T> using
an function to connect the two.
- RasterGeneratorBridge(RasterGenerator<V>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class RasterGeneratorBridge
-
- RasterGeneratorDelegateToDisplayStack<T> - Class in org.anchoranalysis.image.io.stack.output.generator
-
- RasterGeneratorDelegateToDisplayStack(SingleFileTypeGenerator<T, DisplayStack>, boolean) - Constructor for class RasterGeneratorDelegateToDisplayStack
-
- RasterGeneratorDelegateToRaster<S,T> - Class in org.anchoranalysis.image.io.stack.output.generator
-
- RasterGeneratorDelegateToRaster(RasterGenerator<S>) - Constructor for class RasterGeneratorDelegateToRaster
-
- RasterGeneratorSelectFormat<T> - Class in org.anchoranalysis.image.io.stack.output.generator
-
A
RasterGenerator that selects an appropriate output-format based upon each generated
image.
- RasterGeneratorSelectFormat() - Constructor for class RasterGeneratorSelectFormat
-
- rasterResizing() - Method in class InterpolatorFactory
-
An
Interpolator that is suitable for resizing a raster-image with a
range of
intensity values.
- RasterTask<S,U> - Class in org.anchoranalysis.plugin.image.task.bean
-
An experiment that takes (primarily) a series of raster images as an input.
- RasterTask() - Constructor for class RasterTask
-
- RatioFirstToSecond - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Ratio of first-object to second-object in a pair.
- RatioFirstToSecond() - Constructor for class RatioFirstToSecond
-
- RatioNonMode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- RatioNonMode() - Constructor for class RatioNonMode
-
- RatioPrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
Calculates the ratio of prinicpal-axis length using Image Moments.
- RatioPrincipalAxisLength() - Constructor for class RatioPrincipalAxisLength
-
- RatioThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
-
- RatioThreshold() - Constructor for class RatioThreshold
-
- read(Path, Logger) - Method in interface AnnotationReader
-
Reads an annotation, if possible, from the file-system.
- read(Path, Logger) - Method in class ImageLabelAnnotationReader
-
- read(Path, Logger) - Method in class DualMarksAnnotationReader
-
- read(Path) - Method in class CSVReader
-
Opens a CSV for reading.
- read(CSVReaderByLine.ProcessCSVLine) - Method in class ReadByLine
-
Reads a CSV-file iterating through each row and passing it to lineProcessor
- ReadableTuple3i - Interface in org.anchoranalysis.spatial.point
-
A tuple with three-values, respectively for the X, Y and Z dimensions.
- readAcquisitionDate(Path) - Static method in class AcquisitionDateReader
-
Reads an image acquisition-date from a file identified by path, based on the present of EXIF
data.
- readAcquisitionDate(Metadata) - Static method in class AcquisitionDateReader
-
Reads an image acquisition-date from metadata, based on the present of EXIF data.
- ReadAnnotationFromFile - Class in org.anchoranalysis.plugin.annotation.bean.strategy
-
- readAssumeExists(Path, Logger) - Static method in class ReadAnnotationFromFile
-
- ReadByLine - Class in org.anchoranalysis.io.input.csv
-
- ReadByLine(Path, CSVReader) - Constructor for class ReadByLine
-
- readCheckExists(Path, Logger) - Static method in class ReadAnnotationFromFile
-
- readDate(Metadata, Class<T>, int[], int[]) - Static method in class ReadMetadataUtilities
-
Reads a metadata entry of type Date from the first directory of type directoryType.
- readDate(Directory, int) - Static method in class ReadMetadataUtilities
-
Reads a metadata entry of type Date from a Directory.
- readDefaultMarks(Path, Logger) - Method in class DualMarksAnnotationReader
-
- readFileAsString(Path) - Static method in class TextFileReader
-
Reads all the lines in a text-file into a string.
- readFromCSV(Path, boolean) - Static method in class FileLabelMap
-
- readFromFile(Path) - Static method in class Dictionary
-
- ReadFromFile - Class in org.anchoranalysis.io.input.bean.dictionary
-
- ReadFromFile() - Constructor for class ReadFromFile
-
- readFromWidthHeightTags(Metadata, Class<T>, int, int) - Static method in class ReadMetadataUtilities
-
Reads two metadata entries, representing width and height, and use them to form a
Extent.
- readFromWidthHeightTags(Directory, int, int) - Static method in class ReadMetadataUtilities
-
Reads two metadata entries, representing width and height, and use them to form a
Extent.
- readHistogramFromFile(Path) - Static method in class HistogramCSVReader
-
- readInt(Metadata, Class<T>, int) - Static method in class ReadMetadataUtilities
-
Reads a metadata entry of type int from the first directory of type directoryType.
- readInt(Directory, int) - Static method in class ReadMetadataUtilities
-
Reads a metadata entry of type int from a Directory.
- readLine() - Method in class CSVReader.OpenedCSVFile
-
- readLinesAsList(Path) - Static method in class TextFileReader
-
Reads all the lines in a text-file into a list of strings.
- readMetadata(Path) - Static method in class ReadMetadataUtilities
-
Reads metadata, if it exists, from an image.
- readMetadata(Path, boolean) - Static method in class ReadVoxelExtentXml
-
Looks for a metadata file describing the resolution
- ReadMetadataUtilities - Class in org.anchoranalysis.io.bioformats.metadata
-
Reads various image properties from tags in Metadata.
- ReadOptions - Class in org.anchoranalysis.io.bioformats.bean.options
-
- ReadOptions() - Constructor for class ReadOptions
-
- ReadOptionsDelegate - Class in org.anchoranalysis.io.bioformats.bean.options
-
Forces a particular settings, but otherwise uses settings from a delegate
- ReadOptionsDelegate() - Constructor for class ReadOptionsDelegate
-
- readResolutionXml(File) - Static method in class ResolutionAsXml
-
- readStack(Path, Logger) - Method in class StackReader
-
Opens a file at path that should contain only a single-stack.
- ReadVoxelExtentXml - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
Reads
Resolution from an XML file associated an image.
- ReadVoxelExtentXml() - Constructor for class ReadVoxelExtentXml
-
- reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class GrayscaleReconstruction2DIJ
-
- reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class GrayscaleReconstructionByErosion
-
- reconstruction(VoxelsUntyped, VoxelsUntyped, Optional<ObjectMask>) - Method in class GrayscaleReconstructionRobinson
-
- recordCopiedOutput(Path, Optional<Path>, int) - Method in class RecordingCounter
-
Records an copy operation in the log / CSV path mapping.
- RecordedExecutionTimes - Class in org.anchoranalysis.core.time
-
Recorded execution-times for operations.
- RecordedExecutionTimes(Stream<RecordedExecutionTimes.RecordedOperation>) - Constructor for class RecordedExecutionTimes
-
Create with the running-times.
- RecordedExecutionTimes.RecordedOperation - Class in org.anchoranalysis.core.time
-
A particular type of operation that has been recorded (en aggregate).
- RecordedOperation(String, int, double, double, int) - Constructor for class RecordedExecutionTimes.RecordedOperation
-
- RecordedOutputs - Class in org.anchoranalysis.io.output.recorded
-
Outputs recorded from RecordOutputNamesForWriter.
- RecordedOutputs() - Constructor for class RecordedOutputs
-
- recordedOutputs() - Method in class RecordingWriters
-
If defined, all output-names that are passed as arguments to both writers are recorded here.
- RecordedOutputsWithRules - Class in org.anchoranalysis.io.output.recorded
-
Rules to determine what outputting occurs, together with maybe an entity that records the
output-names that are used when writing / querying.
- RecordedOutputsWithRules() - Constructor for class RecordedOutputsWithRules
-
Creates with no rules or outputs defined.
- RecordedOutputsWithRules(MultiLevelRecordedOutputs, MultiLevelOutputEnabled, OutputEnabledDelta) - Constructor for class RecordedOutputsWithRules
-
Creates with all elements defined.
- recordedTimes() - Method in class ExecutionTimeRecorder
-
The execution-times that have been recorded.
- recordedTimes() - Method in class ExecutionTimeRecorderIgnore
-
- recordError(Class<?>, String, Throwable) - Method in interface ErrorReporter
-
Reports an error that occurred as an exception, with a message first introducing it.
- recordError(Class<?>, Throwable) - Method in interface ErrorReporter
-
Reports an error that occurred as an exception
- recordError(Class<?>, String) - Method in interface ErrorReporter
-
Reports an error with a constant string error message.
- recordError(Class<?>, Throwable) - Method in class ErrorReporterBase
-
- recordError(Class<?>, String) - Method in class ErrorReporterBase
-
- recordError(Class<?>, String, Throwable) - Method in class ErrorReporterBase
-
- recordError(Class<?>, Throwable) - Method in class ErrorReporterForTask
-
- recordError(Class<?>, String) - Method in class ErrorReporterForTask
-
- recordError(Class<?>, String, Throwable) - Method in class ErrorReporterForTask
-
- recordErrorFormatted(Class<?>, String, Object...) - Method in interface ErrorReporter
-
Reports an error with a string derived from a format-string.
- recordExecutionTime(String, long) - Method in class ExecutionTimeRecorder
-
Records the execution-time of a particular operation.
- recordExecutionTime(String, CheckedRunnable<E>) - Method in class ExecutionTimeRecorder
-
Executes an operation while recording the execution-time - with a return type.
- recordExecutionTime(String, CheckedSupplier<T, E>) - Method in class ExecutionTimeRecorder
-
Executes an operation while recording the execution-time - with a return type.
- recordExecutionTime(String, long) - Method in class ExecutionTimeRecorderIgnore
-
- RecordingCounter<T> - Class in org.anchoranalysis.plugin.io.shared
-
A counter that also records a manifest of copied outputs in a message-log and CSV file.
- RecordingCounter(Counter, Outputter, T) - Constructor for class RecordingCounter
-
- RecordingWriters - Class in org.anchoranalysis.io.output.recorded
-
Two writers that record any output-names that are passed as arguments.
- RecordingWriters(ElementOutputter, Optional<WriterExecuteBeforeEveryOperation>, Optional<MultiLevelRecordedOutputs>) - Constructor for class RecordingWriters
-
Creates the two writers.
- recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in class MutableDirectory
-
- recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in class DualWriterOperationRecorder
-
- recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in interface WriteOperationRecorder
-
Records a subdirectory that has been recated.
- recordTimeDifferenceBetween(String, long, long) - Method in class ExecutionTimeRecorder
-
Records the execution-time of a particular operation by subtracting the start-time from the
end time.
- recordWarning(String) - Method in interface ErrorReporter
-
Reports an warning with a constant string error message.
- recordWarning(String) - Method in class ErrorReporterBase
-
- recordWarning(String) - Method in class ErrorReporterForTask
-
- recordWarningFormatted(String, Object...) - Method in interface ErrorReporter
-
Reports an warning with a string derived from a format-string.
- recordWrittenFile(String, ManifestDescription, Path, String) - Method in class JobRootDirectory
-
- recordWrittenFile(String, ManifestDescription, Path, String) - Method in class RootDirectory
-
- recordWrittenFile(String, ManifestDescription, Path, String) - Method in class Subdirectory
-
- recordWrittenFile(String, ManifestDescription, Path, String) - Method in class DualWriterOperationRecorder
-
- recordWrittenFile(String, ManifestDescription, Path, String) - Method in interface WriteOperationRecorder
-
Records a file written.
- RecursivelyDescribeExceptionStack - Class in org.anchoranalysis.core.exception.friendly
-
Generates a nice string representation of an Exception and its causes according to certain rules.
- RED - Static variable in class RGBChannelNames
-
Name for the red channel.
- red() - Method in class RGBStack
-
The red channel.
- reduce() - Method in class HungarianAlgorithm
-
Reduce the cost matrix by subtracting the smallest element of each row from all elements of
the row as well as the smallest element of each column from all elements of the column.
- reduce(List<LabelledWithConfidence<ObjectMask>>, Extent, ExecutionTimeRecorder) - Method in class ThresholdConfidence
-
- ReduceFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
- ReduceFirstAndSecond() - Constructor for class ReduceFirstAndSecond
-
- ReduceRatioFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
- ReduceRatioFirstAndSecond() - Constructor for class ReduceRatioFirstAndSecond
-
- Reference<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
-
Uses another feature to calculate the value.
- Reference(String) - Constructor for class Reference
-
Create with a specific identifier.
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
- Reference(String) - Constructor for class Reference
-
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
-
- Reference(String) - Constructor for class Reference
-
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
- Reference(String) - Constructor for class Reference
-
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
- Reference(String) - Constructor for class Reference
-
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.image.bean.stack.provider
-
Retrieves an existing stack.
- Reference(String) - Constructor for class Reference
-
- Reference() - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
- Reference() - Constructor for class Reference
-
- Reference(String) - Constructor for class Reference
-
- Reference - Class in org.anchoranalysis.plugin.points.bean.fitter
-
- Reference() - Constructor for class Reference
-
- ReferenceFactory - Class in org.anchoranalysis.plugin.image.provider
-
Creates reference (i.e.
- ReferenceOrElse - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Returns a object-collection by name if it exists, or else calls objectsElse if it doesn't
exist.
- ReferenceOrElse() - Constructor for class ReferenceOrElse
-
- ReferenceOrEmpty - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
Returns an existing marks-collection or an empty set if it doesn't exist
- ReferenceOrEmpty() - Constructor for class ReferenceOrEmpty
-
- ReferencingFeatureListProvider<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
-
A base class for implementations of
FeatureListProvider that may reference features
created elsewhere.
- ReferencingFeatureListProvider() - Constructor for class ReferencingFeatureListProvider
-
- ReflectInAxesWithinDistance - Class in org.anchoranalysis.plugin.points.bean.fitter
-
Reflects points in each axes if all points are within a certain distance from it
- ReflectInAxesWithinDistance() - Constructor for class ReflectInAxesWithinDistance
-
- reflectThroughOrigin() - Method in class BoundingBox
-
Reflects the bounding box through the origin.
- RegEx - Class in org.anchoranalysis.bean.shared.regex
-
The regular-expression to use for matching groups.
- RegEx() - Constructor for class RegEx
-
- RegExList - Class in org.anchoranalysis.bean.shared.regex
-
Combines one or more
RegEx together, by successively trying to match each
RegEx
until success.
- RegExList() - Constructor for class RegExList
-
- RegExMatcher - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
- RegExMatcher() - Constructor for class RegExMatcher
-
- RegExSimple - Class in org.anchoranalysis.bean.shared.regex
-
Matches a Java-style regular expression against the string.
- RegExSimple(String) - Constructor for class RegExSimple
-
Creates with an expression that should match one or more groups.
- RegExSimple() - Constructor for class RegExSimple
-
- RegExSimple(String, Pattern) - Constructor for class RegExSimple
-
- region() - Method in interface AnnotationWithMarks
-
The region(s) of the marks that specifies the annotation.
- region() - Method in class DualMarksAnnotation
-
- region(BoundingBox, boolean) - Method in class Mask
-
Creates an
ObjectMask corresponding to the on/off state in a bounding-box.
- region(BoundingBox, boolean) - Method in class BoundedVoxels
-
A (sub-)region of the voxels.
- region(BoundingBox, boolean) - Method in interface VoxelsExtracter
-
A (sub-)region of the voxels.
- region(BoundingBox, boolean) - Method in class ObjectMask
-
A (sub-)region of the object-mask.
- regionIntersecting(BoundingBox, int) - Method in class BoundedVoxels
-
- regionIntersecting(BoundingBox) - Method in class ObjectMask
-
Creates an object-mask covering the a bounding-box (that is required to intersect at least
partially)
- RegionMap - Class in org.anchoranalysis.mpp.bean.regionmap
-
Maps integer IDs to sub-regions in the map
- RegionMap(int) - Constructor for class RegionMap
-
- RegionMap() - Constructor for class RegionMap
-
- RegionMapSingleton - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembership - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembership(int) - Constructor for class RegionMembership
-
- RegionMembership() - Constructor for class RegionMembership
-
- RegionMembershipAnd - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembershipAnd() - Constructor for class RegionMembershipAnd
-
- RegionMembershipAnd(int) - Constructor for class RegionMembershipAnd
-
- RegionMembershipOr - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembershipOr() - Constructor for class RegionMembershipOr
-
- RegionMembershipUtilities - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembershipWithFlags - Class in org.anchoranalysis.mpp.bean.regionmap
-
- RegionMembershipWithFlags(RegionMembership, int) - Constructor for class RegionMembershipWithFlags
-
- regionZ(int, int, VoxelsFactoryTypeBound<T>) - Method in class BoundedVoxels
-
Creates an box with a subrange of the slices.
- regionZ(int, int) - Method in class ObjectMask
-
Creates an object-mask with a subrange of the slices.
- register(String, AnchorBeanFactory) - Static method in class RegisterBeanFactories
-
Registers a specific factory.
- register(String, Function<List<T>, Object>) - Static method in class RegisterBeanFactories
-
Registers a bean that creates a {link java.util.List}.
- registerAllPackageBeanFactories() - Static method in class RegisterBeanFactories
-
Registers the factories for the beans that exist in this package
- RegisterBeanFactories - Class in org.anchoranalysis.bean.xml
-
Utility class for registering the Bean-factories that are found in anchor-bean (or any other).
- registerBeanFactories() - Static method in class RegisterBeanFactoriesImage
-
- RegisterBeanFactoriesImage - Class in org.anchoranalysis.image.bean
-
Registers beans that needs particular factories
- RegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.group.parser
-
- RegularExpression() - Constructor for class RegularExpression
-
- RegularExpressionBase - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
- RegularExpressionBase() - Constructor for class RegularExpressionBase
-
- rejected() - Method in interface DualMarks
-
The rejected marks.
- RejectIfConditionXYResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
If the XY resolution of an opened-image meets a certain condition then the resolution is scaled
by a factor.
- RejectIfConditionXYResolution() - Constructor for class RejectIfConditionXYResolution
-
- RejectIfIntensityLessThan - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
- RejectIfIntensityLessThan() - Constructor for class RejectIfIntensityLessThan
-
- RejectIfNotConnected - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
-
Rejects a set of objects, if any object is not fully connected (pixels form two or more separate
connected components)
- RejectIfNotConnected() - Constructor for class RejectIfNotConnected
-
- rejectProposal() - Method in class OptimizationStep
-
- relation() - Method in class RelationToConstant
-
- relation() - Method in class RelationToThreshold
-
The relation to the threshold.
- relation() - Method in class BinaryNotOffVoxels
-
- relation() - Method in class BinaryNotOnVoxels
-
- relation() - Method in class BinaryOffVoxels
-
- relation() - Method in class BinaryOnVoxels
-
- RelationBean - Class in org.anchoranalysis.bean.shared.relation
-
Base class that specifies a
relation between two
doubles.
- RelationBean() - Constructor for class RelationBean
-
- RelationToConstant - Class in org.anchoranalysis.bean.shared.relation.threshold
-
Defines a constant threshold, and a relation to it.
- RelationToConstant() - Constructor for class RelationToConstant
-
- RelationToConstant(RelationBean, double) - Constructor for class RelationToConstant
-
- RelationToThreshold - Class in org.anchoranalysis.bean.shared.relation.threshold
-
A base class specifying threshold and a relation to it, allowing for tests of a value in relation
to a threshold.
- RelationToThreshold() - Constructor for class RelationToThreshold
-
- RelationWithMatches - Class in org.anchoranalysis.plugin.image.bean.object.filter.collective
-
Matches each object with others, and keeps only those where a relation holds true for all matches
(in terms of features)
- RelationWithMatches() - Constructor for class RelationWithMatches
-
- relativeMaskTo(BoundingBox) - Method in class ObjectMask
-
Creates a new object-mask with coordinates changed to be relative to another box.
- relativePath() - Method in class MutableDirectory
-
- relativePath() - Method in class RootDirectory
-
- relativePath() - Method in class SubdirectoryBase
-
- relativePositionTo(BoundingBox) - Method in class BoundingBox
-
The relative position of the corner to another bounding box.
- relativePositionToBox(BoundingBox) - Method in class BoundingBox
-
A new bounding-box using relative position coordinates to another box.
- relativeScale(Extent, Extent, boolean) - Static method in class RelativeScaleCalculator
-
- relativeScale(Extent, Extent) - Static method in class RelativeScaleCalculator
-
Calculates a scaling factor so as to scale source to target.
- RelativeScaleCalculator - Class in org.anchoranalysis.spatial.scale
-
Determine the scaling-factor needed to scale an
Extent to become equal in size to another
Extent.
- relativeScalePreserveAspectRatio(Extent, Extent) - Static method in class RelativeScaleCalculator
-
Calculates a scaling factor so as to maximally scale source to target -
while preserving the aspect ratio.
- RelativeToDirectory - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
Constructs a name by finding the relative-path between the file and the input-directory.
- RelativeToDirectory() - Constructor for class RelativeToDirectory
-
- releaseKeepBest() - Method in class DualState
-
- releaseKeepBest() - Method in class OptimizationStep
-
- rememberConverted(NamedChannelsInput, U, StringBuilder) - Method in class SharedStateRememberConverted
-
Remembers a converted input.
- remove(int) - Method in class ColorList
-
Remove an element at a particular index.
- remove(T) - Method in class IntersectingObjects
-
Removes an object-mask, so that it is no longer considered in queries.
- remove(int) - Method in class ObjectCollection
-
Removes the object at the specified position in the collection.
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in class RandomCollectionWithAddCriteria
-
- remove(EnergyMemoList, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown
-
- remove(EnergyMemoList, int, VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown
-
- remove(int) - Method in class MarksWithEnergyBreakdown
-
- remove(int) - Method in class MarksWithTotalEnergy
-
- remove(int, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy
-
- remove(VoxelizedMarkMemo, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy
-
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in class EnergySavedPairs
-
- remove(EnergySavedInd, int) - Method in class EnergyMemoList
-
- remove(int) - Method in class MemoList
-
- remove(VoxelizedMarkMemo) - Method in class MemoList
-
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in class UpdatableMarksList
-
- remove(Object) - Method in class UpdatableMarksList
-
- remove(int) - Method in class UpdatableMarksList
-
- remove(int) - Method in class ColoredMarks
-
- remove(int) - Method in class MarkCollection
-
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in interface UpdatableMarks
-
- remove(int) - Method in class ColoredOverlayCollection
-
- remove(int) - Method in class OverlayCollection
-
- remove(BoundingBox, T) - Method in class BoundingBoxRTree
-
Removes a particular item from the r-tree, identified by its bounding-box and payload.
- remove(double, double, T) - Method in class IntervalRTree
-
Removes a particular item from the r-tree, identified by its interval and payload.
- remove(Rectangle, T) - Method in class RTree
-
Removes a particular item from the r-tree, identified by its Rectangle and payload.
- removeAll(Collection<?>) - Method in class UpdatableMarksList
-
- removeAndUpdateEnergy(MarksFromPartition, ProposerContext) - Method in class KernelDeathPartition
-
- removeAndUpdateEnergy(T, ProposerContext) - Method in class KernelDeath
-
- removeAndUpdateEnergy(VoxelizedMarksWithEnergy, ProposerContext) - Method in class KernelDeathVoxelized
-
- removeBelowThreshold(int) - Method in class Histogram
-
All values less than threshold are removed.
- removeClosestToUnitZ() - Method in class ImageMoments
-
Removes the entry that is closest to having an eigenVector in direction (0,0,1).
- removeEdge(V, V) - Method in class GraphWithoutPayload
-
Remove an edge between two vertices.
- removeEdge(V, V) - Method in class GraphWithPayload
-
Remove an edge between two vertices.
- removeExtension(String) - Static method in class ExtensionUtilities
-
Removes an extension from a filename or path.
- removeExtension(Path) - Static method in class ExtensionUtilities
-
- RemoveExtension - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
Removes extensions from the identifier (but not from the file) and only if the extension
hasn't already been removed upstream.
- RemoveExtension(FileNamer) - Constructor for class RemoveExtension
-
- RemoveExtension() - Constructor for class RemoveExtension
-
- removeIfExists(T) - Method in class NameValueMap
-
Removes an element from the set, if it exists.
- removeIfExists(FeatureList<FeatureInput>) - Method in class SharedFeatures
-
Remove all features, if they currently exist, from features.
- RemoveIntersectingVoxels - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
-
Considers all possible pairs of objects in a provider, and removes any intersecting pixels
- RemoveIntersectingVoxels() - Constructor for class RemoveIntersectingVoxels
-
- removeIntersectingVoxels(ObjectCollection, Dimensions, boolean) - Static method in class ObjectIntersectionRemover
-
- removeLeadingPeriod(String[]) - Static method in class FormatExtensions
-
Creates a set of extensions with the leading period.
- removeLeft(int) - Method in class ContiguousVoxelPath
-
Removes the first numToRemove pixels from the left
- RemoveMatching - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- RemoveMatching() - Constructor for class RemoveMatching
-
- removeNonMatching(List<T>) - Method in class FilterDescriptiveNameEqualsContains
-
- removeOrReplace(boolean, boolean, boolean) - Method in class MergeCandidate
-
Chops of one-side of keep, and one-side of merge
- RemovePartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
-
- RemovePartition() - Constructor for class RemovePartition
-
- RemovePartitionAndThen<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
-
- RemovePartitionAndThen() - Constructor for class RemovePartitionAndThen
-
- removeRight(int) - Method in class ContiguousVoxelPath
-
Removes the last numToRemove pixels from the right
- RemoveTouchingBorder - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
-
Considers all possible pairs of objects in a provider, and removes those that touch the border.
- RemoveTouchingBorder() - Constructor for class RemoveTouchingBorder
-
- removeTouchingBorderXY(Extent) - Method in class OverlappingObjects
-
Removes any objects from the assignment if they touch the X or Y scene border.
- RemoveTrailingDirectory - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive
-
- RemoveTrailingDirectory() - Constructor for class RemoveTrailingDirectory
-
- removeTwo(EnergyMemoList, int, int, EnergyStackWithoutParameters) - Method in class MarksWithEnergyBreakdown
-
- removeTwo(int, int, EnergyStackWithoutParameters) - Method in class VoxelizedMarksWithEnergy
-
- removeTwo(EnergySavedInd, int, int) - Method in class EnergyMemoList
-
- removeTwo(int, int) - Method in class MarkCollection
-
- removeVertex(V) - Method in class GraphWithoutPayload
-
Removes a vertex and any edges connected to it.
- removeVertex(V) - Method in class GraphWithPayload
-
Removes a vertex and any edges connected to it.
- RemoveWhitespace - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
Removes any whitespace characters from the path
- RemoveWhitespace() - Constructor for class RemoveWhitespace
-
- Repeat - Class in org.anchoranalysis.bean.shared.color.scheme
-
- Repeat() - Constructor for class Repeat
-
- repeat(int, CheckedRunnable<E>) - Static method in class FunctionalIterate
-
Repeats an operation a number of times.
- repeat(int, Supplier<T>) - Static method in class FunctionalList
-
Creates a list of elements, by repeatedly calling the same operation.
- Repeat - Class in org.anchoranalysis.plugin.image.bean.segment.binary
-
- Repeat() - Constructor for class Repeat
-
- Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
-
- Repeat() - Constructor for class Repeat
-
- Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
- Repeat() - Constructor for class Repeat
-
- Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position
-
- Repeat() - Constructor for class Repeat
-
- repeatCountSuccessful(int, CheckedBooleanSupplier<E>) - Static method in class FunctionalIterate
-
Repeats an operation a number of times, counting the number of times the operation returns
true.
- RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
-
Creates a new channel with specific dimensions that repeatedly duplicates a slice from an
existing channel
- RepeatSlice() - Constructor for class RepeatSlice
-
- RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice
-
Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing
mask
- RepeatSlice() - Constructor for class RepeatSlice
-
- repeatUntil(int, CheckedBooleanSupplier<E>) - Static method in class FunctionalIterate
-
Repeats an operation until a true value is returned.
- repeatWithIndex(int, CheckedIntConsumer<E>) - Static method in class FunctionalIterate
-
Repeats an operation a number of times, passing an increment index to operation each
time.
- Replace - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Generates a file-path by replacing all occurrences of a string-pattern with another
- Replace() - Constructor for class Replace
-
- replaceBackslashes(String) - Static method in class SingleFile
-
- replaceBy(BinaryVoxels<UnsignedByteBuffer>) - Method in class Mask
-
Replaces the underlying voxels in the mask with new voxels.
- replaceError(ErrorNode) - Method in class ProposerContext
-
- replaceError(ErrorNode) - Method in class KernelCalculationContext
-
- replaceError(ErrorNode) - Method in class TransformationContext
-
- ReplaceInfinity<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
-
- ReplaceInfinity() - Constructor for class ReplaceInfinity
-
- replaceInput(T) - Method in class SessionInputSequential
-
Replaces existing input with new input
- replaceInputManager(InputManager<?>) - Method in class InputOutputExperiment
-
- ReplaceInputManager - Interface in org.anchoranalysis.experiment.io
-
Indicates and provides a mechanism that the
InputManager can be replaced.
- replaceInputManager(InputManager<?>) - Method in interface ReplaceInputManager
-
- replaceInputManager(InputManager<?>) - Method in class QuickMultiDatasetExperiment
-
- replaceInputManager(InputManager<?>) - Method in class QuickMultiDatasetStructuredExperiment
-
- replaceMaxDirDepth(int) - Method in class PathMatchConstraints
-
- ReplaceNaN<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
-
- ReplaceNaN() - Constructor for class ReplaceNaN
-
- replaceOutputManager(OutputManager) - Method in class InputOutputExperiment
-
- ReplaceOutputManager - Interface in org.anchoranalysis.experiment.io
-
Indicates and provides a mechanism that the
OutputManager can be replaced.
- replaceOutputManager(OutputManager) - Method in interface ReplaceOutputManager
-
- replaceOutputManager(OutputManager) - Method in class QuickMultiDatasetExperiment
-
- replaceOutputManager(OutputManager) - Method in class QuickMultiDatasetStructuredExperiment
-
- ReplacePropertyBeanFactory<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.xml.factory
-
Replaces a property (an XML element of attribute) on a bean before loading it.
- ReplacePropertyBeanFactory(BeanInstanceMap) - Constructor for class ReplacePropertyBeanFactory
-
- replaceSlice(int, VoxelBuffer<T>) - Method in class BoundedVoxels
-
Assigns a new buffer for a slice.
- replaceSlice(int, VoxelBuffer<UnsignedByteBuffer>) - Method in class FromByte
-
- replaceSlice(int, VoxelBuffer<FloatBuffer>) - Method in class FromFloat
-
- replaceSlice(int, VoxelBuffer<UnsignedIntBuffer>) - Method in class FromInt
-
- replaceSlice(int, VoxelBuffer<UnsignedShortBuffer>) - Method in class FromShort
-
- replaceSlice(int, VoxelBuffer<T>) - Method in interface SliceBufferIndex
-
Replaces the voxels for a particular z-slice.
- replaceSlice(int, VoxelBuffer<T>) - Method in class Voxels
-
Assigns a new buffer for a particular slice.
- replaceSlice(int, VoxelsUntyped, int, boolean) - Method in class VoxelsUntyped
-
Copies one particular z-slice of voxels from a source into the current voxels.
- ReplaceStrategy<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.replace
-
- replaceTask(Task<T, S>) - Method in class InputOutputExperiment
-
- replaceTask(Task<T, S>) - Method in class JobProcessor
-
- ReplaceTask<T extends InputFromManager,S> - Interface in org.anchoranalysis.experiment.io
-
Indicates and provides a mechanism that the
Task can be replaced.
- replaceTask(Task<T, S>) - Method in interface ReplaceTask
-
- replaceTask(Task<U, S>) - Method in class ConvertNamedChannels
-
- ReplaceUnusualValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
-
Calculates the underlying feature, but replaces the result with a constant if it happens to be an
"unusual" value
- ReplaceUnusualValue() - Constructor for class ReplaceUnusualValue
-
- replaceVoxels(Voxels<?>) - Method in class Channel
-
Assigns new voxels to replace the existing voxels.
- replaceVoxels(Voxels<T>) - Method in class BoundedVoxels
-
Replaces the voxels in the box.
- replaceVoxels(Voxels<UnsignedByteBuffer>) - Method in class ObjectMask
-
Replaces the voxels in the object-mask.
- reportBegin(FeedbackBeginParameters<T>) - Method in class FeedbackReceiverList
-
- reportBegin(FeedbackBeginParameters<T>) - Method in class FeedbackReceiverRequireArguments
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class PeriodicSubdirectoryReporter
-
- reportBegin(FeedbackBeginParameters<T>) - Method in class ReporterAggregate
-
- reportBegin(FeedbackBeginParameters<T>) - Method in interface FeedbackReceiver
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAggregatedReporter
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterAggregated
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter
-
- reportBegin(FeedbackBeginParameters<T>) - Method in class NullReporter
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class ObjectSerializerPeriodicReporter
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class OptimizationStepLogReporter
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class TextFile
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class TextFileMarksReporter
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class TiffTimeSeries
-
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter
-
- reportEnd(FeedbackEndParameters<T>) - Method in class FeedbackReceiverList
-
- reportEnd(FeedbackEndParameters<T>) - Method in class FeedbackReceiverRequireArguments
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class PeriodicSubdirectoryReporter
-
- reportEnd(FeedbackEndParameters<T>) - Method in class ReporterAggregate
-
- reportEnd(FeedbackEndParameters<T>) - Method in interface FeedbackReceiver
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class ConsoleAggregatedReporter
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterAggregated
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter
-
- reportEnd(FeedbackEndParameters<T>) - Method in class NullReporter
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class OptimizationStepLogReporter
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class TextFile
-
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter
-
- ReporterAggregate<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
-
- ReporterAggregate(double) - Constructor for class ReporterAggregate
-
- ReporterAggregate() - Constructor for class ReporterAggregate
-
- ReporterException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback
-
- ReporterException(String) - Constructor for exception ReporterException
-
- ReporterException(Throwable) - Constructor for exception ReporterException
-
- ReporterInterval<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
-
- ReporterInterval() - Constructor for class ReporterInterval
-
- ReporterInterval(double) - Constructor for class ReporterInterval
-
- ReportFeature<T> - Class in org.anchoranalysis.io.output.bean
-
- ReportFeature() - Constructor for class ReportFeature
-
- ReportFeatureEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureEvaluator() - Constructor for class ReportFeatureEvaluator
-
- ReportFeatureForManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
-
- ReportFeatureForManifest() - Constructor for class ReportFeatureForManifest
-
- ReportFeatureForManifestFileBase - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
-
- ReportFeatureForManifestFileBase() - Constructor for class ReportFeatureForManifestFileBase
-
- ReportFeatureForMarks<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureForMarks() - Constructor for class ReportFeatureForMarks
-
- ReportFeatureForSharedObjects - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureForSharedObjects() - Constructor for class ReportFeatureForSharedObjects
-
- ReportFeatureOnMark - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureOnMark() - Constructor for class ReportFeatureOnMark
-
- ReportFeatureOnMarks - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureOnMarks() - Constructor for class ReportFeatureOnMarks
-
- ReportFeatureOnObject - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureOnObject() - Constructor for class ReportFeatureOnObject
-
- ReportFeatureOnObjectCollection - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureOnObjectCollection() - Constructor for class ReportFeatureOnObjectCollection
-
- ReportFeatureOnObjectsBase<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureOnObjectsBase() - Constructor for class ReportFeatureOnObjectsBase
-
- ReportFeatureWrapError - Class in org.anchoranalysis.mpp.io.bean.report.feature
-
- ReportFeatureWrapError() - Constructor for class ReportFeatureWrapError
-
- reporting(int, StateReporter<T, U>, TransformationContext) - Method in class OptimizationStep
-
- Reporting<S> - Class in org.anchoranalysis.mpp.segment.optimization.step
-
Exposes data which is only needed by reporting tools
- reportItr(Reporting<T>) - Method in class FeedbackReceiverList
-
- reportItr(Reporting<T>) - Method in class FeedbackReceiverRequireArguments
-
- reportItr(Reporting<T>) - Method in class ReporterInterval
-
- reportItr(Reporting<T>) - Method in interface FeedbackReceiver
-
- reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted
-
- reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest
-
- reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter
-
- reportItr(Reporting<T>) - Method in class NullReporter
-
- reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter
-
- reportNewBest(Reporting<T>) - Method in class FeedbackReceiverList
-
- reportNewBest(Reporting<T>) - Method in class FeedbackReceiverRequireArguments
-
- reportNewBest(Reporting<T>) - Method in interface FeedbackReceiver
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class ConsoleAccepted
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class ConsoleAggregatedReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class CSVReporterAggregated
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class CSVReporterBest
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class KernelIterDescriptionSerializerPeriodicReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class Log4JReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class MemoryUsageReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class MinimalExecutionTimeStatsReporter
-
- reportNewBest(Reporting<T>) - Method in class NullReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class OptimizationStepLogReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class TextFile
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class TextFileMarksReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class TiffTimeSeries
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksChangeReporter
-
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class VoxelizedMarksPeriodicReporter
-
- requestOmitExperimentIdentifier() - Method in class OutputArguments
-
- requestOmitExperimentIdentifier() - Method in class OutputPrefixerSettings
-
- requestOutputIncrementingNumberSequence() - Method in class OutputArguments
-
- requestOutputIncrementingNumberSequence() - Method in class OutputPrefixerSettings
-
- requestOutputSuppressDirectories() - Method in class OutputArguments
-
- requestOutputSuppressDirectories() - Method in class OutputPrefixerSettings
-
- RequireArguments - Class in org.anchoranalysis.experiment.bean.require
-
- RequireArguments() - Constructor for class RequireArguments
-
- RequireDebugMode - Class in org.anchoranalysis.experiment.bean.require
-
- RequireDebugMode() - Constructor for class RequireDebugMode
-
- RequireFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
-
- RequireFeatureRelationThreshold() - Constructor for class RequireFeatureRelationThreshold
-
- requiresImageMetadata() - Method in class SummarizerImageMetadata
-
- requiresImageMetadata() - Method in class ExtractIdentifier
-
- requiresImageMetadata() - Method in class ExtractIdentifierAndPath
-
- requiresImageMetadata() - Method in class ExtractPath
-
- requiresImageMetadata() - Method in class SummarizerPath
-
- requiresImageMetadata() - Method in class Summarizer
-
- requiresImageMetadata() - Method in class SummarizerAggregate
-
- requiresImageMetadata() - Method in class SummarizerCount
-
- requiresImageMetadata() - Method in class SummarizerListMultiline
-
- requiresImageMetadata() - Method in class SummarizerSplitMoreThan
-
- reset() - Method in class CachedSupplierBase
-
Ensures the object is unevaluated, deleting any cached result if it exists.
- reset() - Method in class RunningSum
-
Reset the sum and count to zero.
- reset() - Method in class RunningSumCollection
-
Resets all items to zero.
- reset() - Method in class Histogram
-
Sets the count for all values to 0.
- reset() - Method in class VoxelizedMarkMemo
-
- reset() - Method in class AggIDCounter
-
- reset() - Method in class Aggregator
-
- reset() - Method in class PeriodTriggerBank
-
- resetInd() - Method in class EnergySavedInd
-
- ResettableCalculation - Interface in org.anchoranalysis.feature.calculate.cache
-
A calculation that be invalidated (resetted), removing any existing cached value.
- resizedXY(int, int, Interpolator) - Method in interface VoxelsExtracter
-
Creates a new voxels that are a resized version of the current voxels (only in X and Y
dimensions), interpolating as needed.
- resizeXY(Extent) - Method in class Channel
-
Resizes the dimensions of the channel, interpolating the existing voxel values to match.
- resizeXY(Extent, Interpolator) - Method in class Channel
-
- resizeXY(int, int) - Method in class Channel
-
- resizeXY(int, int, Interpolator) - Method in class Channel
-
- resizeXY(int, int) - Method in class Dimensions
-
Resizes the dimensions to have new sizes in the X and Y dimension.
- resolution() - Method in class EnergyStack
-
The image-resolution associated with the energy-stack.
- resolution() - Method in class Channel
-
The resolution of the voxel that describes a physical size for each voxel.
- resolution() - Method in class Dimensions
-
Resolution of voxels to physical measurements.
- resolution(Resolution) - Method in enum OrientationChange
-
A
Resolution that describes
resolution after the orientation change.
- Resolution - Class in org.anchoranalysis.image.core.dimensions
-
The resolution of an image.
- Resolution() - Constructor for class Resolution
-
Creates with a default resolution with value 1.0 in each dimension.
- Resolution(double, double, double) - Constructor for class Resolution
-
Creates with a resolution from three double values for each dimension.
- Resolution(Tuple3d) - Constructor for class Resolution
-
Constructs a resolution from a tuple.
- resolution() - Method in class Mask
-
Resolution of voxels to physical measurements.
- resolution() - Method in class DisplayStack
-
Resolution of voxels to physical measurements.
- resolution() - Method in class Stack
-
Resolution of voxels to physical measurements.
- ResolutionAsXml - Class in org.anchoranalysis.plugin.io.xml
-
Reads and writes a metadata XML file specifying the image-resolution.
- resolutionRequired() - Method in class MergeBase
-
- resolve(Path, Path) - Static method in class ResolvePathAbsolute
-
- resolve(Optional<UnitConverter>, DirectionVector) - Method in class DistancePhysical
-
- resolve(Optional<UnitConverter>, DirectionVector) - Method in class DistanceVoxels
-
- resolve(Optional<UnitConverter>, Point3d, Point3d) - Method in class UnitValueDistance
-
- resolve(Optional<UnitConverter>, Point3i, Point3i) - Method in class UnitValueDistance
-
- resolve(Optional<UnitConverter>, DirectionVector) - Method in class UnitValueDistance
-
- resolve(Optional<Resolution>, boolean) - Method in class Bound
-
- resolveArea(double, Optional<Resolution>) - Method in class FeatureSingleMemoRegion
-
- resolveArea(double, Optional<Resolution>) - Method in class UnitConverter
-
Convert area into another unit representation
- ResolvedBound - Class in org.anchoranalysis.mpp.bean.bound
-
A bound resolved into pixel units
- ResolvedBound(ResolvedBound) - Constructor for class ResolvedBound
-
- ResolvedBound() - Constructor for class ResolvedBound
-
- ResolvedBound(double, double) - Constructor for class ResolvedBound
-
- resolveDistance(double, Optional<Resolution>, DirectionVector) - Method in class UnitConverter
-
Convert distance into another unit representation
- ResolvedPart<S,T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.cache.part
-
Like a
CalculationPart but has been resolved against a cache to reuse any existing
identical instance.
- ResolvedPart(CalculationPart<S, T>) - Constructor for class ResolvedPart
-
- ResolvedPartMap<S,T extends FeatureInput,U> - Class in org.anchoranalysis.feature.calculate.cache.part
-
- ResolvedPartMap(CalculationPartMap<S, T, U, FeatureCalculationException>) - Constructor for class ResolvedPartMap
-
Creates with a map.
- resolveFeatureIdentifier(String) - Method in interface FeatureSymbolCalculator
-
- resolveForAxis(Optional<UnitConverter>, Axis) - Method in class UnitValueDistance
-
Resolves the distance in a direction aligned to a particular axis
- resolveName(String) - Method in class DefineAdderWithPrefixBean
-
Prepends a prefix before the name.
- resolvePath(Path) - Method in class PathPrefixer
-
Converts a relative-path to an absolute-path (relative to the file-path associated with this
current bean)
- resolvePath(String) - Method in class PathPrefixer
-
An absolute path to the prefix
- ResolvePathAbsolute - Class in org.anchoranalysis.core.system.path
-
- resolver() - Method in interface FeatureCalculationInput
-
A resolver for calculations.
- resolver() - Method in class SessionInputSequential
-
- resolveTestPath(String) - Method in class TestLoader
-
Resolves a path to test-data (relative path to the test-data root) to an absolute path on the
file system.
- resolveToVoxels(Optional<UnitConverter>) - Method in class AreaPhysical
-
- resolveToVoxels(Optional<UnitConverter>) - Method in class AreaPixels
-
- resolveToVoxels(Optional<UnitConverter>) - Method in class UnitValueAreaOrVolume
-
Resolves a measurement of area/volume (in whatever units) to units corresponding to the image
pixels/voxels.
- resolveToVoxels(Optional<UnitConverter>) - Method in class VolumePhysical
-
- resolveToVoxels(Optional<UnitConverter>) - Method in class VolumeVoxels
-
- resolveVolume(double, Optional<Resolution>) - Method in class FeatureSingleMemoRegion
-
- resolveVolume(double, Optional<Resolution>) - Method in class UnitConverter
-
Convert volume into another unit representation
- resources() - Method in class LauncherConfig
-
Config for resources sued by the launcher
- Resources - Class in org.anchoranalysis.launcher.resources
-
Accesses resource-files associated with this application.
- Resources(ClassLoader, String, String, String, String, Optional<String>) - Constructor for class Resources
-
- ResultsVector - Class in org.anchoranalysis.feature.results
-
A vector of results of applying a feature-calculations to many entities.
- ResultsVector(int) - Constructor for class ResultsVector
-
Creates with a particular size.
- ResultsVectorList - Class in org.anchoranalysis.feature.results
-
- ResultsVectorList(ResultsVector) - Constructor for class ResultsVectorList
-
Creates with the list containing a single item.
- ResultsVectorList() - Constructor for class ResultsVectorList
-
- ResultsVectorTestUtilities - Class in org.anchoranalysis.test.feature.plugins
-
- ResultsVectorWithThumbnail - Class in org.anchoranalysis.plugin.image.task.feature
-
A results-vector with an optional thumbnails associated with it.
- ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector, OperationFailedException>) - Constructor for class ResultsVectorWithThumbnail
-
- ResultsVectorWithThumbnail(CheckedSupplier<ResultsVector, OperationFailedException>, CheckedSupplier<Optional<DisplayStack>, OperationFailedException>) - Constructor for class ResultsVectorWithThumbnail
-
- retainAll(Collection<?>) - Method in class UpdatableMarksList
-
- RetrieveDestinationFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
-
- RetrieveDestinationFromDual() - Constructor for class RetrieveDestinationFromDual
-
- RetrieveDestinationFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
-
- RetrieveDestinationFromVoxelized() - Constructor for class RetrieveDestinationFromVoxelized
-
- RetrieveSingleMarkOnly - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
-
Retrieves a mark from a marks, assuming there is only one mark in a marks, otherwise throwing an
exception
- RetrieveSingleMarkOnly() - Constructor for class RetrieveSingleMarkOnly
-
- RetrieveSourceFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
-
- RetrieveSourceFromDual() - Constructor for class RetrieveSourceFromDual
-
- RetrieveSourceFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
-
- RetrieveSourceFromVoxelized() - Constructor for class RetrieveSourceFromVoxelized
-
- reuseByte(Voxels<UnsignedByteBuffer>) - Static method in class BinaryVoxelsFactory
-
- reuseByte(Voxels<UnsignedByteBuffer>, BinaryValuesInt) - Static method in class BinaryVoxelsFactory
-
Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have
only two intensity-values representing off and on.
- reuseInt(Voxels<UnsignedIntBuffer>, BinaryValuesInt) - Static method in class BinaryVoxelsFactory
-
Reuses an existing voxel-buffer (of type unsigned int) as a binary-version which should have
only two intensity-values representing off and on.
- ReuseSingletonStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.replace
-
Always re-use a singleton SessionInput, invalidating it each time a new call occurs
- ReuseSingletonStrategy(CacheCreator) - Constructor for class ReuseSingletonStrategy
-
Constructor with default means of creating a session-input
- ReuseSingletonStrategy(CacheCreator, ChildCacheFinder) - Constructor for class ReuseSingletonStrategy
-
Constructor with custom means of creating a session-input
- reverse() - Method in class MergeCandidate
-
- reverseIterateArray(T[], CheckedConsumer<T, E>) - Static method in class FunctionalIterate
-
Iterates through every element in an array in reverse order
- rewind() - Method in class UnsignedByteBuffer
-
- rgb(boolean) - Method in class StackWriteAttributes
-
- rgb(boolean, boolean) - Static method in class StackWriteAttributesFactory
-
- RGB - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Converts a set of channels to a single RGB-stack.
- RGB() - Constructor for class RGB
-
- RGBChannelNames - Class in org.anchoranalysis.image.core.stack
-
Constants for referring to the channels in a RGB-stack or RGBA-stack.
- RGBColor - Class in org.anchoranalysis.core.color
-
- RGBColor() - Constructor for class RGBColor
-
Create with black color.
- RGBColor(Color) - Constructor for class RGBColor
-
- RGBColor(int) - Constructor for class RGBColor
-
Creates with an RGB value encoded as an int, as in the constructor for
Color.
- RGBColor(int, int, int) - Constructor for class RGBColor
-
Creates with specific values for the red, green and blue components.
- RGBColorBean - Class in org.anchoranalysis.bean.shared.color
-
- RGBColorBean() - Constructor for class RGBColorBean
-
Creates with a completely black color.
- RGBColorBean(RGBColor) - Constructor for class RGBColorBean
-
- RGBColorBean(Color) - Constructor for class RGBColorBean
-
- RGBColorBean(int, int, int) - Constructor for class RGBColorBean
-
Create from values for red, green and blue.
- rgbMaybe3D(boolean) - Static method in class StackWriteAttributesFactory
-
- RGBStack - Class in org.anchoranalysis.image.core.stack
-
A stack with exactly three channels, respectively for red, green and blue
colors.
- RGBStack(Dimensions, ChannelFactorySingleType) - Constructor for class RGBStack
-
Creates a particularly-sized stack with all channels initialized to 0.
- RGBStack(Stack) - Constructor for class RGBStack
-
Creates from an existing stack (which must have 1 or 3 channels).
- RGBStack(Channel, Channel, Channel) - Constructor for class RGBStack
-
Create with
Channels for each color.
- RGBTimeSeriesGenerator - Class in org.anchoranalysis.image.io.stack.output.generator
-
- RGBTimeSeriesGenerator(StackWriteOptions) - Constructor for class RGBTimeSeriesGenerator
-
- rightSize() - Method in class OverlappingObjects
-
The total number of objects in the right set.
- rmv(int) - Method in class EnergySavedInd
-
- rmvFromUpdatablePairList(UpdatableMarksList, Mark) - Method in class VoxelizedMarksWithEnergy
-
- rootDirectory(InputContextParameters) - Method in class FilesProvider
-
A root directory for these files, if it exists.
- rootDirectory(InputContextParameters) - Method in class FilesProviderUnary
-
- rootDirectory(InputContextParameters) - Method in class FilesProviderWithDirectory
-
- rootDirectory(InputContextParameters) - Method in class FilesProviderWithoutDirectory
-
- rootDirectory(InputContextParameters) - Method in class SpecificPathList
-
- RootDirectory - Class in org.anchoranalysis.io.manifest.directory
-
- RootDirectory() - Constructor for class RootDirectory
-
- RootDirectory(Path) - Constructor for class RootDirectory
-
- rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class PathPrefixer
-
Provides a prefix that becomes the root-folder.
- rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class PathPrefixerAvoidResolve
-
- rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class HomeSubdirectory
-
- rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class Rooted
-
- rootDirectoryPrefix(Optional<String>, PathPrefixerContext) - Method in class ExperimentStructure
-
- rootDirectoryPrefixAvoidResolve(Optional<String>) - Method in class PathPrefixerAvoidResolve
-
Provides a prefix that becomes the root-folder.
- Rooted - Class in org.anchoranalysis.plugin.io.bean.file.path.prefixer
-
Prepend a 'root' before the file-path-prefix obtained from a delegate
- Rooted() - Constructor for class Rooted
-
- Rooted(PathPrefixerAvoidResolve, String) - Constructor for class Rooted
-
- Rooted - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
Represents a set of files, with a different path-root depending on context.
- Rooted() - Constructor for class Rooted
-
- Rooted - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
- Rooted() - Constructor for class Rooted
-
- RootedExperiment - Class in org.anchoranalysis.plugin.quick.bean.structure
-
- RootedExperiment() - Constructor for class RootedExperiment
-
- RootedFilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
-
- RootedFilePath() - Constructor for class RootedFilePath
-
- RootedFilePathUtilities - Class in org.anchoranalysis.plugin.io.input.path
-
- RootFilePathRegEx - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
-
- RootFilePathRegEx() - Constructor for class RootFilePathRegEx
-
- RootPath - Class in org.anchoranalysis.bean.shared.path
-
Defines a root path.
- RootPath() - Constructor for class RootPath
-
- RootPathMap - Class in org.anchoranalysis.plugin.io.input.path
-
A collection of root-paths indexed by their name.
- RotatableBoundingBox - Class in org.anchoranalysis.mpp.mark.points
-
A two-dimensional bounding-box rotated at arbitrary angle in XY plane around a point.
- RotatableBoundingBox() - Constructor for class RotatableBoundingBox
-
- RotatableBoundingBoxFactory - Class in org.anchoranalysis.mpp.mark.points
-
- RotateImageToMatchEXIFOrientation - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
Rotates an image to match any EXIF orientation information, if it exists.
- RotateImageToMatchEXIFOrientation() - Constructor for class RotateImageToMatchEXIFOrientation
-
- RotateImageToMatchEXIFOrientation(StackReaderOrientationCorrection) - Constructor for class RotateImageToMatchEXIFOrientation
-
- rotatePoint(Tuple3d) - Method in class RotationMatrix
-
Performs a rotation on a single point, encoded as a
Point3d.
- rotatePointInplace(Point3d) - Method in class RotationMatrix
-
Performs a rotation on a single point, replacing the existing value of the point.
- RotationMatrix - Class in org.anchoranalysis.spatial.orientation
-
A
matrix that performs a rotation in
Euclidean space.
- RotationMatrix(int) - Constructor for class RotationMatrix
-
Creates a rotation-matrix populated only with zeros.
- RotationMatrix(DoubleMatrix2D) - Constructor for class RotationMatrix
-
Creates a rotation-matrix from an existing DoubleMatrix2D.
- RowLabels - Class in org.anchoranalysis.feature.io.csv
-
Labels for each row of feature-results in the outputted CSV row.
- RowLabels(String) - Constructor for class RowLabels
-
Creates with a single string as an identifier.
- RowLabels(Optional<String[]>, Optional<MultiName>) - Constructor for class RowLabels
-
- RTree<T> - Class in org.anchoranalysis.spatial.rtree
-
Bases class for implementations of R-Trees that store objects with associated geometry.
- RTree(int) - Constructor for class RTree
-
Creates an empty R-Tree.
- RTree(int, int) - Constructor for class RTree
-
Creates an empty R-Tree with a specified number of children.
- run() - Method in interface CheckedRunnable
-
- runCommandLineApplication(String[], LauncherConfig, Logger) - Static method in class Launch
-
Runs a command-line application, by parsing arguments, and then executing an experiment.
- runExperiment(String) - Method in class ExperimentLauncherFromShell
-
Runs an experiment identified by an XML found in the resources
- runExperiment(String, Optional<String>, Optional<String>) - Method in class ExperimentLauncherFromShell
-
Runs an experiment identified by an XML found in the resources
- runExperimentInTemporaryDirectory(String, Path) - Method in class ExperimentLauncherFromShell
-
Creates a temporary-folder, copies data all data from the associated test-loader, and runs an
experiment
- runExperimentInTemporaryDirectory(String, Optional<String>, Optional<String>, Path, String[]) - Method in class ExperimentLauncherFromShell
-
Creates a temporary-folder, copies data all data from the associated test-loader, and runs an
experiment
- RunningSum - Class in org.anchoranalysis.math.arithmetic
-
Mutable class that allows for incrementing jointly sum and count variables, so as to eventually
calculate the mean.
- RunningSum() - Constructor for class RunningSum
-
- RunningSum(double, long) - Constructor for class RunningSum
-
- RunningSumCollection - Class in org.anchoranalysis.math.arithmetic
-
A collection of
RunningSum where an operation is executed on all objects in the
collection.
- RunningSumCollection(int) - Constructor for class RunningSumCollection
-
Constructor.
- RunningSumExtrema - Class in org.anchoranalysis.math.arithmetic
-
Like a
RunningSum but also remembers the
mean and
max across all the added
values.
- RunningSumExtrema() - Constructor for class RunningSumExtrema
-
- RunningSumParented - Class in org.anchoranalysis.experiment.time
-
Wraps a
RunningSum with an additional variable, indicating the total number of parent
operations.
- RunningSumParented(int) - Constructor for class RunningSumParented
-
- RunningSumPoint - Class in org.anchoranalysis.spatial.point
-
A running sum for tracking points separately in each dimension.
- RunningSumPoint() - Constructor for class RunningSumPoint
-
- runTaskAndCompareOutputs(T, V, Path, String, Iterable<String>) - Static method in class TaskSingleInputHelper
-
Executes a task on a single-input.
- sampleDoubleFromRange(double) - Method in interface RandomNumberGenerator
-
Generates a uniformly random floating-point number within a range from 0
(exclusive) to endExclusive.
- sampleDoubleFromRange(double, double) - Method in interface RandomNumberGenerator
-
Generates a uniformly random floating-point number within a range.
- sampleDoubleFromZeroCenteredRange(double) - Method in interface RandomNumberGenerator
-
Generates a uniformly random floating-point number centered around 0 ranging from
[-halfWidth,+halfWidth] (both exclusive).
- sampleDoubleZeroAndOne() - Method in interface RandomNumberGenerator
-
Samples from a uniformly-distributed range between 0.0 (exclusive) and 1.0
(exclusive).
- sampleDoubleZeroAndOne() - Method in class RandomNumberGeneratorMersenne
-
- sampleFromAvailable(int) - Method in class PartitionedMarks
-
Samples from the available marks
- sampleFromList(List<T>) - Method in interface RandomNumberGenerator
-
Samples uniformly an element from a list.
- sampleInteger(int) - Method in class ProposerContext
-
Samples an integer uniformally between [0..maxVal)
- sampleIntFromRange(int) - Method in interface RandomNumberGenerator
-
Generates a uniformly random discrete number within a range from 0 (inclusive) to
endExclusive.
- sampleIntFromRange(int, int) - Method in interface RandomNumberGenerator
-
Samples from a uniformly random discrete number within a range.
- sampleLongFromRange(long) - Method in interface RandomNumberGenerator
-
Generates a uniformly random discrete number within a range from 0 (inclusive) to
endExclusive.
- sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class RandomCollectionWithAddCriteria
-
- sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class RandomCollection
-
- SampleWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- SampleWithDirectory() - Constructor for class SampleWithDirectory
-
- ScalarProposer - Class in org.anchoranalysis.mpp.bean.proposer
-
- ScalarProposer() - Constructor for class ScalarProposer
-
- ScalarThreeDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
Like a
IntConsumer but accepts three coordinates of a point as scalar arguments.
- ScalarTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
Like a
IntConsumer but accepts two coordinates of a point as scalar arguments.
- scale(ScaleFactor, Interpolator, Optional<Extent>) - Method in class BoundedVoxels
-
Creates a scaled-version (in XY dimensions only) of the current bounding-box.
- scale(ScaleFactor) - Method in class ObjectMask
-
Produces a scaled-version of an object-mask.
- scale(ScaleFactor, Optional<Extent>) - Method in class ObjectMask
-
Produces a scaled-version of an object-mask.
- scale(double) - Method in class Bound
-
- scale(double) - Method in class BoundMinMax
-
- scale(double) - Method in class ResolvedBound
-
- scale(ScaleFactor) - Method in class Ellipse
-
- scale(ScaleFactor) - Method in class Ellipsoid
-
- scale(ScaleFactor) - Method in class MarkWithPositionAndSingleRadius
-
Objects are scaled in pre-rotated position.
- scale(ScaleFactor) - Method in class Mark
-
Scales the mark in X and Y dimensions.
- scale(ScaleFactor) - Method in class MarkWithPosition
-
- scale(ScaleFactor) - Method in class LineSegment
-
- scale(ScaleFactor) - Method in class PointList
-
- scale(ScaleFactor) - Method in class Polygon
-
- scale(ScaleFactor) - Method in class PolygonCurve
-
- scale(ScaleFactor) - Method in class RotatableBoundingBox
-
- scale(Channel, ScaleCalculator, Interpolator, Optional<ImageSizeSuggestion>, MessageLogger) - Static method in class ScaleXY
-
- scale(Mask, ScaleCalculator, Optional<ImageSizeSuggestion>) - Static method in class ScaleXY
-
- Scale - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Scales all the objects in the collection by a particular scale-factor.
- Scale() - Constructor for class Scale
-
- Scale - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
-
- Scale() - Constructor for class Scale
-
- scale(ScaleFactor) - Method in class BoundingBox
-
Scales the bounding-box, both the corner-point and the extent.
- scale(ScaleFactor, Extent) - Method in class BoundingBox
-
Scales the bounding-box corner-point, and assigns a new extent.
- scale(double) - Method in class Point2d
-
Arithmetically multiplies each dimension's value by a factor.
- scale(double) - Method in class Point2f
-
Multiplies each dimension's component by a factor.
- scale(double) - Method in class Tuple3d
-
Arithmetically multiply values across each dimension.
- scale(int) - Method in class Tuple3i
-
Arithmetically multiplies by a value across each dimension.
- scale(double) - Method in class Tuple3i
-
Arithmetically multiplies by a value across each dimension.
- scale(Point3d) - Method in class ScaleFactor
-
Multiplies a
Point3d by the respective scaling-factor in each X and Y dimensions.
- scale(int, int) - Method in class ScaleFactorInt
-
Multiplies a point by the respective scaling-factor in each dimension.
- scale(Point2i) - Method in class ScaleFactorInt
-
Multiplies a
Point2i by the respective scaling-factor in each dimension.
- scale(Extent) - Method in class ScaleFactorInt
-
Multiplies an
Extent by the respective scaling-factor in each dimension.
- scale(ScaleFactor, Point3i) - Static method in class Scaler
-
Scales a point in XY by multiplying each dimension by its corresponding scaling-factor.
- ScaleableBackground - Class in org.anchoranalysis.image.io.stack.output.box
-
A stack that can be used as a background (and maybe scaled).
- scaleBy(DisplayStack, ScaleFactor, Interpolator) - Static method in class ScaleableBackground
-
Creates a background from a stack with scaling
- ScaleByDictionary - Class in org.anchoranalysis.plugin.image.bean.channel.convert
-
Scales by compressing a certain range of values into the 8-bit signal.
- ScaleByDictionary() - Constructor for class ScaleByDictionary
-
- ScaleByMinMaxValue - Class in org.anchoranalysis.plugin.image.bean.channel.convert
-
Scales by compressing a certain range of values into the 8-bit signal
- ScaleByMinMaxValue() - Constructor for class ScaleByMinMaxValue
-
- ScaleByTypeToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert
-
- ScaleByTypeToByte() - Constructor for class ScaleByTypeToByte
-
- ScaleCalculator - Class in org.anchoranalysis.image.bean.spatial
-
Calculating a scaling-factor from dimensions.
- ScaleCalculator() - Constructor for class ScaleCalculator
-
- scaleClampTo(ScaleFactor, Extent) - Method in class BoundingBox
-
Scales the bounding-box, both the corner-point and the extent - ensuring it remains inside a
containing-extent.
- ScaledElements<T> - Class in org.anchoranalysis.image.core.object.scale
-
A list of elements, with an
ObjectMask representation, that have been scaled.
- ScaledElements(List<T>, ScaleFactor, ObjectScalingMethod, Optional<UnaryOperator<T>>, Optional<UnaryOperator<T>>, AccessObjectMask<T>) - Constructor for class ScaledElements
-
Creates elements to be scaled.
- scaledObjectFor(T) - Method in class ScaledElements
-
Gets the scaled version of an element given the unscaled element.
- ScaledOverlayCreator - Interface in org.anchoranalysis.overlay.object.scaled
-
Creates a scaled version of
ObjectMask to use as an overlay.
- scaleElements(List<T>, ScaleFactor, AccessObjectMask<T>) - Method in interface ObjectScalingMethod
-
Applies a scaling factor to elements, where each element is associate with a unique
ObjectMask.
- scaleElements(List<T>, ScaleFactor, Optional<UnaryOperator<T>>, Optional<UnaryOperator<T>>, AccessObjectMask<T>) - Method in interface ObjectScalingMethod
-
Applies a scaling factor to elements, where each element is associate with a unique
ObjectMask.
- scaleElements(List<T>, ScaleFactor, boolean, Extent, AccessObjectMask<T>) - Static method in class Scaler
-
Scales every element in a list collectively, ensuring the results remain inside a particular
region.
- ScaleFactor - Class in org.anchoranalysis.spatial.scale
-
What to scale X and Y dimensions by.
- ScaleFactor(double) - Constructor for class ScaleFactor
-
Create with an identical scaling-factor for all dimensions.
- ScaleFactor(double, double) - Constructor for class ScaleFactor
-
Create with specific scaling-factors for each dimension.
- ScaleFactorInt - Class in org.anchoranalysis.spatial.scale
-
Like
ScaleFactor but only allows integer scaling-factors in each dimension.
- ScaleFactorInt(int, int) - Constructor for class ScaleFactorInt
-
- ScaleImage - Class in org.anchoranalysis.plugin.image.task.bean.scale
-
Creates a scaled copy of images.
- ScaleImage() - Constructor for class ScaleImage
-
- scaleObjects(ObjectCollection, ScaleFactor) - Static method in class Scaler
-
Scales every object-mask in a collection collectively.
- scaleObjects(ObjectCollection, ScaleFactor, boolean, Extent) - Static method in class Scaler
-
Scales every object-mask in a collection collectively, ensuring the results remain
inside a particular region.
- scaleObjects(ObjectCollection, ScaleFactor, boolean, Optional<UnaryOperator<ObjectMask>>, Optional<UnaryOperator<ObjectMask>>) - Static method in class Scaler
-
Scales every object-mask in a collection collectively (if not overlappjng), allowing
for additional manipulation before and after scaling.
- scaleQuantity(double, int) - Static method in class Scaler
-
Multiplies a quantity (integer) by a scaling-factor, returning it as an integer.
- Scaler - Class in org.anchoranalysis.image.core.object.scale
-
Scales object-masks (or other more generic elements) collectively to avoid undesired overlap.
- Scaler - Class in org.anchoranalysis.spatial.scale
-
- scaleRadii(double) - Method in class Ellipse
-
- ScaleToSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack
-
Create a thumbnail by scales an image to a particular size.
- ScaleToSize() - Constructor for class ScaleToSize
-
- scaleX(double) - Method in class Tuple3i
-
Arithmetically multiplies the X-axis component by a value.
- scaleXY(ScaleFactor) - Method in class DualMarksAnnotation
-
Scales the marks in the annotation in X and Y dimensions.
- scaleXY(ScaleFactor) - Method in class Channel
-
Resizes the dimensions of the channel, by scaling the existing size by a factor.
- scaleXY(ScaleFactor, Interpolator) - Method in class Channel
-
- scaleXY(ScaleFactor) - Method in class Resolution
-
Multiplies the X and Y components of the resolution by a factor.
- scaleXY(ScaleFactor) - Method in class Mask
-
Creates a new
Mask whose X- and Y- dimensions are scaled by
scaleFactor.
- scaleXY(ScaleFactor) - Method in class MarkCollection
-
Scales the mark in X and Y dimensions.
- ScaleXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Scales the channel in the X and Y dimensions.
- ScaleXY() - Constructor for class ScaleXY
-
- ScaleXY - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
Scales the mask in XY dimensions, but not in Z dimension.
- ScaleXY() - Constructor for class ScaleXY
-
- ScaleXY - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
- ScaleXY() - Constructor for class ScaleXY
-
- scaleXY(double) - Method in class Tuple3d
-
Arithmetically multiply values by a factor only in X and Y dimensions.
- scaleXY(double) - Method in class Tuple3i
-
Arithmetically multiplies the X- and Y-axis components by a value.
- scaleXYBy(ScaleFactor) - Method in class Dimensions
-
Scales the X- and Y- dimensions by a scaling-factor.
- scaleXYBy(ScaleFactor) - Method in class Extent
-
Scales the X- and Y- dimensions by a scaling-factor.
- scaleY(double) - Method in class Tuple3i
-
Arithmetically multiplies the Y-axis component by a value.
- scaling - Variable in class ToUnsignedByteWithScaling
-
- sceneContains(Point2i) - Static method in class CircleObjectFixture
-
- ScoreObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
-
- ScoreObjects() - Constructor for class ScoreObjects
-
- ScoreVoxels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
-
Assigns a score (a value indicating how probable something is) to each voxel
- ScoreVoxels() - Constructor for class ScoreVoxels
-
- search(CalculationPart<S, T>) - Method in interface CalculationPartResolver
-
Searches for an equivalent calculation to calculation.
- search(CalculationPartMap<S, T, U, FeatureCalculationException>) - Method in interface CalculationPartResolver
-
Searches for an equivalent calculation to calculation.
- SearchDirectory - Class in org.anchoranalysis.io.input.bean.files
-
Searches a directory for files whose paths match a particular predicate.
- SearchDirectory(String) - Constructor for class SearchDirectory
-
Create for a specific directory.
- SearchDirectory() - Constructor for class SearchDirectory
-
- Second - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Evaluates the first-object in a pair only
- Second(Feature<FeatureInputSingleObject>) - Constructor for class Second
-
- Second() - Constructor for class Second
-
- second(String) - Method in class MultiLevelBinary
-
- second(String) - Method in class MultiLevelNot
-
- second(String) - Method in interface MultiLevelOutputEnabled
-
A second-level of
OutputEnabled for a particular
outputName as used in
first-level.
- second(String) - Method in class OutputEnabledMutable
-
- second(String) - Method in class MultiLevelRecordedOutputs
-
A
RecordedOutputs for recording second-level outputs for a given
outputName
from the first-level.
- secondaryReport() - Method in class StateReporter
-
- secondaryReport() - Method in class StateReporterIdentity
-
- secondaryReport() - Method in class StateReporterToPixelized
-
- secondaryReport() - Method in class StateReporterTransformer
-
- secondEntries() - Method in class MultiLevelRecordedOutputs
-
All second-level recorded output entries.
- secondLevel(String) - Method in class RecordingWriters
-
A writer that performs a second-level check on which outputs occur, but writes to the
top-level directory.
- secondLevelOutputs(String, OutputEnabled) - Method in class OutputEnableRulesSpecify
-
- secondPart() - Method in class CombinedName
-
- secondPart() - Method in interface MultiName
-
The second part of the name.
- secondPart() - Method in class SimpleName
-
- seek(int) - Method in class SlidingBuffer
-
Moves buffer to a particular z-slice.
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentation
-
Performs a segmentation on voxels so that each voxel has an on or off state
after the operation.
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationOne
-
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationReference
-
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class BinarySegmentationThreshold
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class SegmentChannelIntoObjects
-
Segments a channel to produce an object-collection.
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class SegmentChannelIntoObjectsUnary
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class SegmentChannelIntoObjectsUnary
-
- segment(SharedObjects, Optional<Dictionary>, InputOutputContext) - Method in class SegmentIntoMarks
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class AtScale
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class ConnectedComponentsFromBinarySegmentation
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class Filter
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class ImposeMinima
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class Mser
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>, SegmentChannelIntoObjects) - Method in class SegmentOnMaximumIntensityAndExpandInZ
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class WatershedYeong
-
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class Sequence
-
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class ThresholdAgainstChannel
-
- segment(Channel, Optional<ObjectMask>, Optional<ObjectCollection>) - Method in class FloodFillEachIntensityLevel
-
- segment(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class SegmentThresholdAboveMinBound
-
- segment(SharedObjects, Optional<Dictionary>, InputOutputContext) - Method in class SegmentWithMarkedPointProcess
-
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholder
-
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholderMask
-
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class SliceThresholderWithoutMask
-
- SegmentationBean<T> - Class in org.anchoranalysis.image.bean.segment
-
Performs some kind of segmentation on an image.
- SegmentationBean() - Constructor for class SegmentationBean
-
- SegmentationFailedException - Exception in org.anchoranalysis.image.bean.nonbean.error
-
- SegmentationFailedException(String) - Constructor for exception SegmentationFailedException
-
- SegmentationFailedException(String, Throwable) - Constructor for exception SegmentationFailedException
-
- SegmentationFailedException(Throwable) - Constructor for exception SegmentationFailedException
-
- SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment
-
- SegmentChannel() - Constructor for class SegmentChannel
-
- SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
- SegmentChannel() - Constructor for class SegmentChannel
-
- SegmentChannelByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Performs segmentation of a channel using each object in the upstream collection as a mask.
- SegmentChannelByObject() - Constructor for class SegmentChannelByObject
-
- SegmentChannelIntoObjects - Class in org.anchoranalysis.image.bean.segment.object
-
A base class for algorithms to segment a channel into one or more objects.
- SegmentChannelIntoObjects() - Constructor for class SegmentChannelIntoObjects
-
- SegmentChannelIntoObjectsUnary - Class in org.anchoranalysis.image.bean.segment.object
-
A base-class for segmentations that takes another object-segmentation algorithm as a parameter.
- SegmentChannelIntoObjectsUnary() - Constructor for class SegmentChannelIntoObjectsUnary
-
- segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class BinarySegmentationOne
-
- segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class Invert
-
- segmentFromExistingSegmentation(VoxelsUntyped, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class Repeat
-
- SegmentInstanceWithModel<T extends InferenceModel> - Class in org.anchoranalysis.plugin.image.task.bean.segment
-
Using a model-pool, performs instance segmentation on an image producing zero, one or more
objects per image.
- SegmentInstanceWithModel() - Constructor for class SegmentInstanceWithModel
-
- SegmentIntoMarks - Class in org.anchoranalysis.mpp.segment.bean
-
- SegmentIntoMarks() - Constructor for class SegmentIntoMarks
-
- SegmentMarksFromImage - Class in org.anchoranalysis.plugin.mpp.experiment.bean.segment
-
Segments an image into a collection of
Marks.
- SegmentMarksFromImage() - Constructor for class SegmentMarksFromImage
-
- SegmentMarksState - Class in org.anchoranalysis.plugin.mpp.segment.shared
-
State that only needs to be initialized once can be shared across many calls to the algorithm.
- SegmentMarksState(KernelProposer<VoxelizedMarksWithEnergy, UpdatableMarksList>, Define) - Constructor for class SegmentMarksState
-
- SegmentObjectsFromONNXModel - Class in org.anchoranalysis.plugin.onnx.bean.object.segment.stack
-
Performs instance-segmentation using the ONNX Runtime and an .onnx model file.
- SegmentObjectsFromONNXModel() - Constructor for class SegmentObjectsFromONNXModel
-
- SegmentObjectsFromTensorFlowModel - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack
-
Performs instance-segmentation using OpenCV's DNN module and a TensorFlow
.pb SavedModel file.
- SegmentObjectsFromTensorFlowModel() - Constructor for class SegmentObjectsFromTensorFlowModel
-
- SegmentOnMaximumIntensityAndExpandInZ - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D
segmentation.
- SegmentOnMaximumIntensityAndExpandInZ() - Constructor for class SegmentOnMaximumIntensityAndExpandInZ
-
- SegmentStack<T extends InferenceModel> - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Segments a stack into objects.
- SegmentStack() - Constructor for class SegmentStack
-
- SegmentThresholdAboveMinBound - Class in org.anchoranalysis.plugin.mpp.bean.segment.binary
-
- SegmentThresholdAboveMinBound() - Constructor for class SegmentThresholdAboveMinBound
-
- SegmentWithMarkedPointProcess - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks
-
- SegmentWithMarkedPointProcess() - Constructor for class SegmentWithMarkedPointProcess
-
- SegmentWithSeeds - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Takes each object one-by-one from objectsSource, and finds matching seeds from objectsSeeds
- SegmentWithSeeds() - Constructor for class SegmentWithSeeds
-
- select(ExecutionArguments) - Method in interface SelectParam
-
Retrieves the parameter.
- select(ExecutionArguments) - Method in class UseDefaultManager
-
- selectChannels(ChannelSource, boolean) - Method in class All
-
- selectChannels(ChannelSource, boolean) - Method in class FromStacks
-
Takes a stack-collection and extracts a set of references to particular channels (each with a
name)
- selectChannels(ChannelSource, boolean) - Method in class One
-
- selectChannels(ChannelSource, boolean) - Method in class SpecificAndRename
-
- selectDelegate(StackWriteOptions) - Method in class BranchChannels
-
- selectDelegate(StackWriteOptions) - Method in class BranchStack
-
- selectDelegate(StackWriteOptions) - Method in class BranchSuggestedFormat
-
- selectDelegate(StackWriteOptions) - Method in class StackWriterDelegateBase
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class HDF5ObjectsGenerator
-
- selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class RasterGenerator
-
Selects the file-extension to use for a particular stack.
- selectFileExtension(Stack, StackWriteOptions, OutputWriteSettings, Optional<Logger>) - Method in class RasterGeneratorSelectFormat
-
Combines stack-write-options derived for a particular stack with the general write-options
associated with the
RasterGenerator.
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class RGBTimeSeriesGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class DictionaryGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SerializedGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SingleFileTypeGenerator
-
Selects the file/extension to be used for outputting the file.
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class SingleFileTypeGeneratorBridge
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class CSVGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class StringGenerator
-
- selectFileExtension(OutputWriteSettings, Optional<Logger>) - Method in class XMLGenerator
-
- selectIndexToRmv(MarkCollection, ProposerContext) - Static method in class KernelDeath
-
- selective() - Method in class RecordingWriters
-
A writer that allows only certain selected output-names, and records the written output-names
- selectMarkFrom(MarkCollection, ProposerContext) - Method in class MarkFromCollectionProposer
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class Check
-
- selectMarkFrom(MarkCollection, ProposerContext) - Method in class MarkFromCollectionProposerUnary
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class MarkFromCollectionProposerUnary
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class Repeat
-
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class UniformRandom
-
- selectOutputEnabled(Optional<OutputEnabledRules>) - Method in class RecordedOutputsWithRules
-
- SelectParam<T> - Interface in org.anchoranalysis.launcher.executor.selectparam
-
Different methods of selecting a object T that is used as a parameter for an experiment.
- SelectParamFactory - Class in org.anchoranalysis.launcher.executor.selectparam
-
Creates an appropriate
SelectParam based upon the options passed to the command-line.
- SelectSlicesBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- SelectSlicesBase() - Constructor for class SelectSlicesBase
-
- SelectSlicesWithIndexBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- SelectSlicesWithIndexBase() - Constructor for class SelectSlicesWithIndexBase
-
- separate(Collection<T>) - Method in class SpatiallySeparate
-
Splits a collection of elements into spatially separate clusters, without consuming
all elements in elements.
- Sequence - Class in org.anchoranalysis.plugin.image.bean.segment.binary
-
Performs a sequence of succesive segmentations
- Sequence() - Constructor for class Sequence
-
- SequencedDirectory - Interface in org.anchoranalysis.io.manifest.directory.sequenced
-
- SequencedDirectoryDeserializer<T> - Class in org.anchoranalysis.io.manifest.directory.sequenced
-
Applies a deserializer to each file in a directory with a sequence of files.
- SequencedDirectoryDeserializer(SequencedDirectory, Deserializer<T>, Logger) - Constructor for class SequencedDirectoryDeserializer
-
Creates from a manifest-directory entry.
- SequenceInteger - Class in org.anchoranalysis.bean.permute.property
-
A sequence of integers.
- SequenceInteger() - Constructor for class SequenceInteger
-
- sequenceIterator() - Method in class PermutePropertySequence
-
Iterates each element in sequence.
- SequenceMemory - Class in org.anchoranalysis.io.generator.sequence
-
- SequenceMemory() - Constructor for class SequenceMemory
-
- SequenceType<T> - Class in org.anchoranalysis.io.manifest.sequencetype
-
A sequence of elements (of type T), which are mapped to a range of integer indices.
- SequenceType() - Constructor for class SequenceType
-
- SequenceTypeException - Exception in org.anchoranalysis.io.manifest.sequencetype
-
- SequenceTypeException(String) - Constructor for exception SequenceTypeException
-
- SequenceTypeException(Exception) - Constructor for exception SequenceTypeException
-
- SequentialProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor
-
Executes jobs sequentially
- SequentialProcessor() - Constructor for class SequentialProcessor
-
- SequentialSession<T extends FeatureInput> - Class in org.anchoranalysis.feature.session
-
Calculates features with successively different parameters, taking care of caching etc.
- SerializedGenerator<T> - Class in org.anchoranalysis.io.generator.serialized
-
- SerializedGenerator(Optional<String>) - Constructor for class SerializedGenerator
-
- SerializedObjectSupplier<T> - Interface in org.anchoranalysis.io.manifest.finder
-
Supplies a serialized-object (if it exists)
- serializeObjectToFile(T, Path) - Static method in class XStreamSerializer
-
Writes a file with a serialized representation of an object.
- SessionInputSequential<T extends FeatureInput> - Class in org.anchoranalysis.feature.session
-
- SessionInputSequential(T, CacheCreator) - Constructor for class SessionInputSequential
-
Constructor
- SessionInputSequential(T, CacheCreator, ChildCacheFinder) - Constructor for class SessionInputSequential
-
- set() - Method in class DoubleSet
-
The underlying set of values.
- set() - Method in class IntegerSet
-
The underlying set of values.
- set() - Method in class StringSet
-
The underlying set of values.
- set(int, double) - Method in class ResultsVector
-
Assigns a result at a particular position.
- set(int, ResultsVector) - Method in class ResultsVector
-
Assigns many results, starting at a particular position, and incrementing thereafter.
- set(int, VoxelizedMarkMemo) - Method in class MemoList
-
- set(int, UpdatableMarks) - Method in class UpdatableMarksList
-
- set(int, Mark) - Method in class MarkCollection
-
- setAboveMaxValue(double) - Method in class RangeCompareBase
-
Constant to return if outside the range (above the maximum allowed)
- setAcceptDirectoryErrors(boolean) - Method in class SearchDirectory
-
If true, continues when a directory-access-error occurs (logging it), otherwise throws an
exception.
- setAcceptMissingResolution(boolean) - Method in class WithResolutionBase
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
- setAcceptMissingResolution(boolean) - Method in class VoxelPhysicalSize
-
Whether to throw an exception (if true) if image-resolution is missing, or return Double.Nan (if false).
- setAcceptNoResolution(boolean) - Method in class ReadVoxelExtentXml
-
If false, an exception is thrown if the resolution file is missing for a particular image.
- setAcceptOutsideScene(boolean) - Method in class CheckMarkWithMask
-
- setAdd(DefineAdderBean) - Method in class VisualizeOnBackground
-
- setAddCriteria(AddCriteria<T>) - Method in class RandomCollectionWithAddCriteria
-
- setAdditionalBackgrounds(List<DerivePath>) - Method in class MarkProposerStrategy
-
Additional background-stacks that are possible to use while annotating.
- setAdditionalChannels(List<ChannelEntry>) - Method in class MultiInputManagerQuick
-
Additional channels other than the main one, which are located in the main raster file
- setAdditionalChannels(List<ChannelEntry>) - Method in class NamedChannelsQuick
-
Additional channels other than the main one, which are located in the main raster file
- setAdditionalPropertyPaths(StringSet) - Method in class PermuteProperty
-
Additional property paths that are also changed, together with propertyPath.
- setAddName(boolean) - Method in class CombineCSV
-
- setAddOne(boolean) - Method in class Quantile
-
- setAddSum(int) - Method in class GradientBaseAddSum
-
Added to all gradients (so we can store negative gradients)
- setAdjacentChannels(List<AdjacentFile>) - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file adjacent to the main raster file
- setAggIntervalLog10(double) - Method in class ReporterInterval
-
How many iterations before printing a new report? Encoded in log10.
- setAggregateTriggerBank(AggregateTriggerBank<T>) - Method in class FeedbackBeginParameters
-
- setAll(EnergySavedAll) - Method in class MarksWithEnergyBreakdown
-
Certain features are stored for every object, so that we can reference them in our
calculations for the 'all' component
- setAnnealScheme(AnnealScheme) - Method in class SimulatedAnnealing
-
- setAnnotations(AnnotationInputManager<NamedChannelsInputPart, T>) - Method in class FromAnnotations
-
- setAnnotatorStrategy(S) - Method in class AnnotationInputManager
-
The strategy to be used for annotating.
- setAppendChannels(List<AppendStack>) - Method in class NamedChannelsQuick
-
Channels that are located in a separate raster file somewhere else in the project's structure
- setAppendCSV(DerivePath) - Method in class FromCSVInputManager
-
- setAppendCsv(AppendCsv) - Method in class MatchedAppendCsv
-
- setAppendDictionary(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendFilePath(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendHistogram(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarks(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarksFromAnnotation(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarksFromAnnotationAcceptedOnly(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendMarksFromAnnotationRejectedOnly(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendObjects(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setAppendStack(List<NamedBean<DerivePath>>) - Method in class MultiInputManager
-
- setApplyResolution(boolean) - Method in class DistanceTransform3D
-
Multiples the values by the x-resolution, if it exists.
- setApplyToPath(boolean) - Method in class MatchRegularExpression
-
If true, the filter is applied to the path as a whole, not just the filename (using forward
slashes as directory separators)
- setArrange(ArrangeStackBean) - Method in class ArrangeRaster
-
- setArrange(ArrangeStack) - Method in class Cell
-
- setArrange(ArrangeStackBean) - Method in class CombineRasterGenerator
-
- setAsMemberFlag(byte, byte) - Static method in class RegionMembershipUtilities
-
- setAsPercentage(boolean) - Method in class Quantile
-
If true, the quantile is interpreted as a percentage rather than a decimal
- setAssigner(AnnotationComparisonAssigner<T>) - Method in class CompareAnnotations
-
- setAssignMode(AssignMode<S, T, U>) - Method in class SimulatedAnnealing
-
- setAvoidBulletOnFirst(boolean) - Method in class SummarizerAggregate
-
Iff true no bullet is added for the very first-item in the list
- setAvoidDivideByZero(boolean) - Method in class Divide
-
- setAvoidOverlappingObjects(boolean) - Method in class PairNeighbors
-
If true, no overlapping objects are treated as pairs
- setAxis(String) - Method in class AxisAlignedUnitVector
-
Which axis the unit-vector will align with.
- setAxis(String) - Method in class CenterOfGravity
-
- setAxis(String) - Method in class GradientForAxis
-
Which axis? X=0, Y=1, Z=2
- setAxis(String) - Method in class ForSpecificAxis
-
- setAxis(String) - Method in class ArbitraryInsidePoint
-
- setAxis(String) - Method in class BoundingBoxAlongAxisBase
-
- setAxis(String) - Method in class GradientMeanForAxis
-
- setAxis(String) - Method in class PrincipalAxisOrientation
-
Which axis to read from (x,y,z)
- setAxis(String) - Method in class BoundingBoxExtent
-
- setAxisColor(RGBColorBean) - Method in class PlotColorScheme
-
- setAxisMax(double) - Method in class AxisLimits
-
- setAxisMin(double) - Method in class AxisLimits
-
- setBackground(AnnotationBackground) - Method in class AnnotatorStrategy
-
The visual background to use while annotating.
- setBackground(Either<Dimensions, DisplayStack>) - Method in class ObjectsAsRGBGenerator
-
A background image or dimensions to define an empty background.
- setBackground(String) - Method in class CompareAnnotations
-
The name of the stack to use as background to the annotations.
- setBackground(ProviderAsStack) - Method in class ColoredBase
-
The background.
- setBackgroundChannelIndex(int) - Method in class OutlinePreserveRelativeSize
-
Uses only this channel (identified by an index in the stack) as the background, -1 disables.
- setBackgroundChannelProvider(ChannelProvider) - Method in class MorphologicalOperatorBase
-
- setBackgroundColor(RGBColorBean) - Method in class PlotColorScheme
-
- setBackgroundID(String) - Method in class VisualizeOnBackground
-
- setBackgroundStackMap(StringMap) - Method in class AnnotationBackground
-
If non-null, maps underlying stack-name to a background.
- setBackgroundStackName(String) - Method in class SegmentIntoMarks
-
- setBeanExtension(String) - Method in class QuickMultiDatasetExperiment
-
- setBeanExtension(String) - Method in class QuickMultiDatasetStructuredExperiment
-
- setBelowMinValue(double) - Method in class RangeCompareBase
-
Constant to return if outside the range (below the minimum allowed)
- setBest(boolean) - Method in class VoxelizedMarksChangeReporter
-
- setBigNeighborhood(boolean) - Method in class Dilate
-
- setBigNeighborhood(boolean) - Method in class ConnectedComponentsFromMask
-
If true uses 8 neighborhood rather than 4 neighborhood etc.
- setBigNeighborhood(boolean) - Method in class DecomposeIntoConnectedComponents
-
if true, uses 8 neighborhood instead of 4, and similarly in 3d
- setBigNeighborhood(boolean) - Method in class Dilate
-
- setBigNeighborhood(boolean) - Method in class TraverseOuterContourOnImage
-
- setBinary(boolean) - Method in class ScaleImage
-
Iff true the image to be scaled is treated as a binary-mask, and interpolation during scaling
ensures only two binary-values are ouputted.
- setBinaryInputChannelID(String) - Method in class AddDistanceTransform
-
The ID of the binary input mask that determines the region of the Watershed.
- setBinarySgmn(BinarySegmentation) - Method in class BinarySegmentByObject
-
- setBirthRepeats(int) - Method in class KernelReplace
-
- setBit0(boolean) - Method in class RegionMembership
-
- setBit1(boolean) - Method in class RegionMembership
-
- setBit2(boolean) - Method in class RegionMembership
-
- setBit3(boolean) - Method in class RegionMembership
-
- setBit4(boolean) - Method in class RegionMembership
-
- setBit5(boolean) - Method in class RegionMembership
-
- setBit6(boolean) - Method in class RegionMembership
-
- setBit7(boolean) - Method in class RegionMembership
-
- setBitsPerPixel(int) - Method in class ForceBitsPerPixel
-
- setBlockSize(SizeXY) - Method in class HOGParameters
-
The block-size as per OpenCV implementation (identical default-size).
- setBlockStride(SizeXY) - Method in class HOGParameters
-
The block-stride as per OpenCV implementation (identical default-size).
- setBlue(int) - Method in class RGBColorBean
-
Sets the blue component value.
- setBlue(int) - Method in class RGBColor
-
Sets the blue component value.
- setBlue(ChannelProvider) - Method in class ThreeChannels
-
- setBold(boolean) - Method in class TextStyle
-
Whether to bold the drawn text
- setBorderWidth(int) - Method in class MontageSlices
-
Adds a border around each part of the montage
- setBounds(BoundRotation) - Method in class RandomOrientation
-
- setBridgeMatcher(ObjectMatcher) - Method in class Bridge
-
Used to match each input-object to an intermediary-object
- setBundleSize(int) - Method in class ObjectSerializerPeriodicReporter
-
- setBundleSize(int) - Method in class VoxelizedMarksChangeReporter
-
- setBySlices(boolean) - Method in class ConnectedComponentsFromMask
-
- setCacheSize(int) - Method in class RelationWithMatches
-
Size of feature evaluation cache for featureEvaluatorMatch
- setCalculateLevel(CalculateLevel) - Method in class CalculateLevelOne
-
- setCalculateLevel(CalculateLevel) - Method in class ThresholderGlobal
-
- setCalculateLevel(CalculateLevel) - Method in class LevelPerObjectBase
-
Method to calculate the level for a particular object.
- setCalculateLevel(CalculateLevel) - Method in class GreaterThanThreshold
-
Calculates the level for the threshold
- setCalculateLevel(CalculateLevel) - Method in class LevelFromHistogram
-
- setCalculateLevel(CalculateLevel) - Method in class ThresholdHistogram
-
- setCalculateLevel(CalculateLevel) - Method in class CalculateLevelBase
-
- setCalculateLevelElse(CalculateLevel) - Method in class CalculateLevelRelativeToThreshold
-
- setCaseSensitive(boolean) - Method in class PatternSpan
-
Iff true, a case sensitive search is used to match patterns.
- setCellDefault(ArrangeStackBean) - Method in class Tile
-
- setCells(List<Cell>) - Method in class Tile
-
- setCellSize(SizeXY) - Method in class HOGParameters
-
The cell-size as per OpenCV implementation (identical default-size).
- setCenterPoint(Point3d) - Method in class FitResult
-
- setChangeExisting(boolean) - Method in class ConvertBase
-
If true, the existing channel can be changed.
- setChannel(ChannelProvider) - Method in class ChannelProviderUnary
-
- setChannel(ChannelProvider) - Method in class ChannelFilter
-
- setChannel(ChannelProvider) - Method in class FromChannel
-
- setChannel(ChannelProvider) - Method in class FromChannel
-
- setChannel(ChannelProvider) - Method in class FromChannelBase
-
- setChannel(ChannelProvider) - Method in class IntensityGreaterEqualThan
-
- setChannel(ChannelProvider) - Method in class UnaryWithChannelBase
-
- setChannel(ChannelProvider) - Method in class WithChannelBase
-
- setChannel(ChannelProvider) - Method in class FromChannelOrMask
-
A channel that is provided to the stack.
- setChannel1(ChannelProvider) - Method in class ChannelProviderBinary
-
- setChannel1(ChannelProvider) - Method in class ChannelProviderTernary
-
- setChannel2(ChannelProvider) - Method in class ChannelProviderBinary
-
- setChannel2(ChannelProvider) - Method in class ChannelProviderTernary
-
- setChannel3(ChannelProvider) - Method in class ChannelProviderTernary
-
- setChannelAssignFrom(ChannelProvider) - Method in class AssignFromChannel
-
- setChannelConversionStyle(ChannelConvertStyle) - Method in class ConvertImageFormat
-
To convert as RGB or independently or in another way.
- setChannelConverter(ConvertChannelTo<T>) - Method in class Convert
-
- setChannelConverter(ConvertChannelTo<?>) - Method in class ConvertImageFormat
-
Optionally, how to convert from one bit-depth to another (scaling, clamping etc.)
- setChannelElse(ChannelProvider) - Method in class IfParamEquals
-
- setChannelFilter(ChannelFilter) - Method in class ConvertImageFormat
-
Optionally, includes only certain channels when converting.
- setChannelFirst(int) - Method in class Difference
-
Index of first channel
- setChannelGroupID(int) - Method in class RegularExpression
-
- setChannelID(String) - Method in class AddEdgeFilters
-
The ID of the channel that provides the input to the filter
- setChannelIfVoxelZero(ChannelProvider) - Method in class IfVoxelZero
-
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in
this channel instead
- setChannelIndex(int) - Method in class FromStack
-
- setChannelIndex(int) - Method in class FromStackChannel
-
- setChannelIndex(int) - Method in class One
-
- setChannelIndex(int) - Method in class MultiInputManagerQuick
-
If either stackAsChannel==true or we have specified additionalChannels this indicated which
channel to use from the stack
- setChannelLookup(ChannelProvider) - Method in class NormalizeDifferenceToMedian
-
- setChannelMap(ChannelMap) - Method in class NamedChannels
-
- setChannelMask(String) - Method in class ExportImageHistograms
-
If defined, this is the name of channel used as a mask over the values which are fed into the
histogram
- setChannelName(String) - Method in class ChannelFilter
-
- setChannelName(String) - Method in class SingleChannel
-
- setChannelName(String) - Method in class ConvertNamedChannelsToStack
-
By default all channels are converted into a stack.
- setChannelSecond(int) - Method in class Difference
-
Index of second channel
- setChannelsExtra(List<ChannelProvider>) - Method in class ScoreVoxels
-
- setChannelsPerByteArray(int) - Method in class ForceChannelsPerByteArray
-
- setChannelThreshold(ChannelProvider) - Method in class ThresholdAgainstChannel
-
- setCheck(CheckMark) - Method in class Not
-
- setCheckMark(CheckMark) - Method in class FromObjects
-
- setCheckMark(CheckMark) - Method in class Check
-
- setCheckMark(CheckMark) - Method in class Check
-
- setCheckParsedFilePathBag(CheckParsedFilePathBag) - Method in class GroupFiles
-
Imposes a condition on each parsed-file-path-bag which must be-fulfilled if a file is to be
included.
- setClassifierProvider(FeatureListProvider<FeatureInputStack>) - Method in class BinaryClassifierImageLabeller
-
- setClearOutsideMask(boolean) - Method in class ThresholdAgainstChannel
-
- setCol(int) - Method in class Cell
-
- setCollapseFilename(boolean) - Method in class FilePathAppendBase
-
- setColor(RGBColorBean) - Method in class FromSingle
-
The single color to repeat.
- setColor(RGBColorBean) - Method in class AnnotationLabel
-
An optional color associated with the label when displayed via GUI
- setColor(RGBColorBean) - Method in class ColoredMask
-
- setColors(ColorScheme) - Method in class ColorSchemeUnary
-
The delegate that creates the color-list before subsequent processing.
- setColors(List<RGBColorBean>) - Method in class FromList
-
The list of colors to specify.
- setColors(ColorScheme) - Method in class ColoredBaseWithGenerator
-
Colors to use for drawing objects
- setColorScheme(ColorScheme) - Method in class GenerateToMatchObjects
-
- setColorsUnpaired(ColorScheme) - Method in class CompareAnnotations
-
- setColorUnselectedObjects(RGBColorBean) - Method in class OutlinePreserveRelativeSize
-
Optionally outline the other (unselected for the thumbnail) objects in this particular color.
- setColumnDefinition(ColumnDefinition) - Method in class ExportObjectsFromCSV
-
Column definition for the CSV files
- setColumnGroup(String) - Method in class ColumnDefinition
-
Name of CSV column used to group results (the same values, are outputted together)
- setColumnID(String) - Method in class ColumnDefinition
-
Name of CSV column with the file identifier
- setColumns(int) - Method in class MontageSlices
-
How many columns to use in the montage, or 0 to guess an approximately square output
- setColumnUniquePixel(String) - Method in class ColumnDefinition
-
Name of CSV column with X coordinate of point for the first Object
- setCombine(CombineObjectsForFeatures<T>) - Method in class FromObjects
-
- setCommand(String) - Method in class MorphologicalOperation
-
One of: open, close, fill, erode, dilate, skel, outline
- setComparerLeft(ComparableSource) - Method in class AnnotationComparisonInputManager
-
- setComparerRight(ComparableSource) - Method in class AnnotationComparisonInputManager
-
- setCondition(DictionaryCondition) - Method in class IfParamEquals
-
- setCondition(DictionaryCondition) - Method in class IfKeyValueCondition
-
- setConstant(double) - Method in class MaxWithConstant
-
- setContains(String) - Method in class DescriptiveNameContainsImageLabeller
-
- setContains(String) - Method in class FilterDescriptiveName
-
A descriptive-name must contain (case-sensitive) this string.
- setConvert(ConvertChannelToWithHistogram<T>) - Method in class ConvertWithHistogram
-
- setConvexHull(boolean) - Method in class FitPointsFromObjects
-
If true, Reduces the set of points by applying a convex-hull operation
- setCopyFilesNaming(CopyFilesNaming<NoSharedState>) - Method in class CopyFilesNamingOne
-
- setCountThreshold(int) - Method in class SummarizerSplitMoreThan
-
If there are more than countThreshold elements, use summarizerGreaterThan,
else summarizerElse.
- setCov(boolean) - Method in class ObjectRadiusStandardDeviation
-
- setCreateMark(CreateMarkFromPoints) - Method in class PointsFitter
-
- setCreateShort(boolean) - Method in class ArrangeRaster
-
- setCreateShort(boolean) - Method in class GenerateString
-
- setCreateShort(boolean) - Method in class TileWithLabels
-
- setCreateShort(boolean) - Method in class DistanceTransform3D
-
- setCreateShort(boolean) - Method in class DistanceTransformForEachObject3D
-
- setCreateShort(boolean) - Method in class CreateNew
-
If True creates an unsigned short-image
- setCsvFilePath(DerivePath) - Method in class FilterCSVColumn
-
- setCsvIgnoreZeros(boolean) - Method in class ExportImageHistograms
-
Iff true, bins with zero-counts are not written as a row in the CSV file.
- setCurrentTemp(double) - Method in class Geometry
-
- setCustomName(String) - Method in class Feature
-
An optional additional name that be associated with the feature (defaults to an empty
string).
- setDatasetName(String) - Method in class ExperimentResultsExperimentStructure
-
The name of the experiment including version suffix
- setDatasetNameSubdirectory(boolean) - Method in class ExperimentResultsExperimentStructure
-
If true the datasetName is appended as a subdirectory e.g.
- setDatasets(StringSet) - Method in class QuickMultiDatasetExperiment
-
- setDatasets(StringSet) - Method in class QuickMultiDatasetStructuredExperiment
-
- setDatasetSpecific(String) - Method in class QuickMultiDatasetExperiment
-
- setDatasetSpecific(String) - Method in class QuickMultiDatasetStructuredExperiment
-
- setDatasetSuffix(String) - Method in class FilePathAppendBase
-
A suffix appended to the dataset name extracted from the reg exp
- setDatasetVersion(String) - Method in class ExperimentResultsExperimentStructure
-
A version-suffix appended to the dataset name extracted from the reg exp
- setDay(boolean) - Method in class ExperimentIdentifierAuto
-
If true, the current day (yyyy.MM.dd) is included in the output
- setDebug(boolean) - Method in class RootPath
-
If true this root is preferred, when executing a job in debugging mode.
- setDebug(boolean) - Method in class ThresholdedFeature
-
- setDebugModeParameters(Optional<DebugModeParameters>) - Method in class InputContextParameters
-
Parameters for debug-mode (only defined if we are in debug mode)
- setDefaultBehaviourString(Optional<String>) - Method in class ExperimentExecutor
-
If present, a string is printed in the description if the default-experiment is used,
otherwise ignored.
- setDefaultColors(ColorScheme) - Method in class OutputWriteSettings
-
The default color-scheme used for outputs, if no other scheme is specified.
- setDefaultStackReaderForMetadata(StackReader) - Method in class ConvertNamedChannels
-
Supplies to the imageMetadataReader to use, if no other reader is specified.
- setDefine(Define) - Method in class MarkEvaluator
-
- setDefine(Define) - Method in class DefineOutputter
-
- setDefine(DefineOutputter) - Method in class Develop
-
Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
- setDefine(DefineOutputter) - Method in class ExportReportFeaturesFromMulti
-
- setDefine(DefineOutputterWithEnergy) - Method in class FromObjects
-
- setDefine(DefineOutputter) - Method in class ExportObjectsAsCroppedImages
-
- setDefine(DefineOutputterWithEnergy) - Method in class SegmentWithMarkedPointProcess
-
Adds definitions of stacks/objects etc.
- setDelaySizeAtEnd(int) - Method in class MovieFromSlices
-
- setDelegate(ResolvedBound) - Method in class BoundMinMax
-
- setDelimiter(String) - Method in class DirectoryWithPrefix
-
Added between prefix and the filename, if the filename is defined.
- setDelimiter(String) - Method in class SubsetRangeIfRequested
-
Character used to split the name into groups.
- setDelimiter(String) - Method in class LastDirectoryAsPrefix
-
- setDelta(double) - Method in class Mser
-
- setDeltat(double) - Method in class AnisotropicDiffusion
-
the integration constant for the numerical integration scheme.
- setDepth(double) - Method in class ImposeResolution
-
Physical pixel size of a voxel in z-dimension.
- setDerivePath(DerivePath) - Method in class DualMarksAnnotationAsObjects
-
- setDerivePath(DerivePath) - Method in class MarksAsObjects
-
- setDerivePath(DerivePath) - Method in class MaskAsObject
-
Where to find the
Mask to compare, as a function of the source file-path.
- setDerivePath(DerivePath) - Method in class Objects
-
Where to find the objects to compare, as a function of the source file-path.
- setDerivePath(DerivePath) - Method in class CollapseFileName
-
- setDerivePath(DerivePath) - Method in class RemoveTrailingDirectory
-
- setDictionary(DictionaryProvider) - Method in class FeatureEvaluator
-
Parameters to optionally associated with stackEnergy, and meaningless if stackEnergy is not specified.
- setDictionary(DictionaryProvider) - Method in class EnergySchemeCreatorByElement
-
- setDictionary(DictionaryProvider) - Method in class ScaleByDictionary
-
- setDictionary(DictionaryProvider) - Method in class AssignFromDictionary
-
The dictionary from which an assignment will occur.
- setDictionary(DictionaryProvider) - Method in class ScoreVoxels
-
- setDictionary(DictionaryProvider) - Method in class DictionaryCondition
-
The dictionary to provide a value to check.
- setDictionary(DictionaryProvider) - Method in class IfParamEqual
-
- setDictionary(String) - Method in class ParamFromCollection
-
- setDictionary(DictionaryProvider) - Method in class FeatureListProviderLDAClassifier
-
- setDictionary(DictionaryProvider) - Method in class FeatureValueCheckMark
-
- setDictionary(DictionaryProvider) - Method in class DefineOutputterWithEnergy
-
- setDictionary(DictionaryProvider) - Method in class GaussianSampler
-
The dictionary that parameterizes the Gaussian-distribution that is sampled from.
- setDictionary(String) - Method in class Develop
-
If non-empty, the identifier for a dictionary that is treated as part of the energy-stack.
- setDictionary(DictionaryProvider) - Method in class SegmentMarksFromImage
-
If non-empty, a dictionary that is passed to the segmentation procedure.
- setDimensions(DimensionsProvider) - Method in class ReportFeatureForMarks
-
- setDimensions(DimensionsProvider) - Method in class FromDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class FromDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class RepeatSlice
-
Dimensions to create new mask
- setDimensions(DimensionsProvider) - Method in class MergeBase
-
- setDimensions(DimensionsProvider) - Method in class WithDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class WithOptionalDimensionsBase
-
- setDimensions(DimensionsProvider) - Method in class ToDimensions
-
The dimensions the source image/entity is desired to be scaled to.
- setDimensions(DimensionsProvider) - Method in class FromMarks
-
- setDimensions(DimensionsProvider) - Method in class RequireFeatureRelationThreshold
-
- setDimensions(DimensionsProvider) - Method in class PointsFitterToMark
-
- setDimensionsSourceFallback(DimensionsProvider) - Method in class ToDimensions
-
- setDirection(DirectionVectorBean) - Method in class ConvertToPhysicalDistance
-
Direction of the distance being converted, defaults to a unit vector along the X-axis
- setDirection(VectorInDirection) - Method in class FeatureMarkDirection
-
- setDirectionVector(VectorInDirection) - Method in class FromUnitValueDistance
-
- setDirectory(String) - Method in class FilesProviderWithDirectoryString
-
A directory in which to look for files.
- setDirectory(Path) - Method in class DirectoryWithPrefix
-
- setDirectory(String) - Method in class HomeSubdirectory
-
A relative-path (to the user home directory) which is used as an output directory
- setDirectoryDataset(String) - Method in class QuickMultiDatasetExperiment
-
- setDirectoryDistance(int) - Method in class QuickMultiDatasetStructuredExperiment
-
How many directories to recurse back from the current file to the Experiments/ directory
- setDirectoryOutput(String) - Method in class QuickExperiment
-
- setDisableDebugMode(boolean) - Method in class RootedFilePath
-
- setDisableDebugMode(boolean) - Method in class Rooted
-
- setDistance(int) - Method in class LevelPerObjectNeighbors
-
How many neighbors to include by distance (distance==1 implies all directly touching
neighbors, distance==2 implies those touching the directly touching etc.)
- setDistanceMapProvider(ChannelProvider) - Method in class MergeSpatialClusters
-
A distance map which can also be used for making decisions on merging
- setDistanceMax(double) - Method in class CalculateLevel
-
- setDistanceTransformMultiplyBy(float) - Method in class AddDistanceTransform
-
Multiplies the distance transform by this factor to make it more meaningful in a short.
- setDistanceTransformSmoothSigmaMeters(double) - Method in class AddDistanceTransform
-
If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters
below.
- setDistanceX(double) - Method in class ReflectInAxesWithinDistance
-
- setDistanceY(double) - Method in class ReflectInAxesWithinDistance
-
- setDistanceZ(double) - Method in class ReflectInAxesWithinDistance
-
- setDistanceZEndIfEmpty(UnitValueDistance) - Method in class XYOrientationExtendToZ
-
- setDivideByZeroValue(double) - Method in class Divide
-
- setDivisor(double) - Method in class PermutePropertySequenceDouble
-
What to divide the integer-sequence by.
- setDo3D(boolean) - Method in class AnisotropicDiffusion
-
Whether to perform the diffusion in 3D direction, or rather only in the 2D plane.
- setDo3D(boolean) - Method in class ObjectCollectionProviderMorphological
-
- setDo3D(boolean) - Method in class MorphologicalIterations
-
Whether to perform the morphological dimensions in 3D or 2D
- setDo3D(boolean) - Method in class PairNeighbors
-
- setDo3D(boolean) - Method in class TouchingVoxels
-
- setDo3D(boolean) - Method in class Erode
-
- setDo3D(boolean) - Method in class NumberRemovedVoxelsAfterClosing
-
- setDo3D(boolean) - Method in class OutlineKernelBase
-
- setDo3D(boolean) - Method in class UniformRandomRadiiProposer
-
- setDrawReverseLine(boolean) - Method in class Orientation
-
- setDuplicate(boolean) - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting existing data
This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- setDuplicate(boolean) - Method in class Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting
data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- setElemAllCreator(FeatureListProvider<FeatureInputAllMemo>) - Method in class EnergySchemeCreatorByElement
-
- setElemIndCreator(FeatureListProvider<FeatureInputSingleMemo>) - Method in class EnergySchemeCreatorByElement
-
- setElemPairCreator(FeatureListProvider<FeatureInputPairMemo>) - Method in class EnergySchemeCreatorByElement
-
- setEmptyValue(double) - Method in class CenterOfGravity
-
- setEmptyValue(double) - Method in class Intersection
-
- setEmptyValue(double) - Method in class ArbitraryInsidePoint
-
- setEmptyValue(int) - Method in class IntensityMeanMaxSlice
-
- setEmptyValue(double) - Method in class IntensityMeanShellBase
-
- setEmptyValue(double) - Method in class DerivedObject
-
- setEnd(int) - Method in class SequenceInteger
-
An index beyond which we cannot iterate (inclusive).
- setEnd(int) - Method in class IncrementingIntegers
-
- setEnergyChannelIndex(int) - Method in class Identity
-
- setEnergyChannelIndex(int) - Method in class RejectIfIntensityLessThan
-
- setEnergyChannelIndex(int) - Method in class SingleChannel
-
- setEnergyChannelIndex(int) - Method in class QuantileAcrossConnectedComponents
-
- setEnergyChannelIndexCheck(int) - Method in class IdentityImposeValueRelationToHistogram
-
- setEnergyChannelIndexFail(int) - Method in class IdentityImposeValueRelationToHistogram
-
- setEnergyIndex(int) - Method in class NumberNeighboringVoxels
-
Index of which channel in the energy-stack to select
- setEnergyIndex(int) - Method in class SpecificEnergyChannelBase
-
Index of which channel in the energy-stack to select
- setEnergyIndex(int) - Method in class FeatureEnergyChannel
-
Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
- setEnergyIndex(int) - Method in class OutsideRange
-
- setEnergyIndex(int) - Method in class Intensity
-
The channel that that forms the histogram
- setEnergyIndex(int) - Method in class AsObjectMask
-
The channel that that forms an object-mask with the bounding-box set to entire channel's
dimensions
- setEnergyIndex(int) - Method in class OverlapMaskBase
-
- setEnergyIndexGradient(int) - Method in class TextureScore
-
- setEnergyIndexMask(int) - Method in class IntensityMeanShellBase
-
A channel of the energyStack that is used as an additional mask using default byte values for
on and off.
- setEnergyIndexMask(int) - Method in class Intensity
-
Optionally, index of another channel that masks the histogram.
- setEnergyIndexX(int) - Method in class IntensityGradientBase
-
- setEnergyIndexY(int) - Method in class IntensityGradientBase
-
- setEnergyIndexZ(int) - Method in class IntensityGradientBase
-
- setEnergySchemeCreator(EnergySchemeCreator) - Method in class MarkEvaluator
-
- setEnergySchemeCreator(EnergySchemeCreator) - Method in class SegmentWithMarkedPointProcess
-
Creates an energy scheme that assigns an energy score to each collection of marks.
- setEnergyStack(EnergyStack) - Method in class FeatureInputEnergy
-
Assigns an
EnergyStack to be associated with the input.
- setEnergyStack(Optional<EnergyStack>) - Method in class FeatureInputEnergy
-
Assigns an optional
EnergyStack to be associated with the input.
- setEnergyTotal(double) - Method in class MarksWithTotalEnergy
-
The pre-annealed total energy
- setEnergyTotal(double) - Method in class EnergySavedInd
-
- setEquals(String) - Method in class FilterDescriptiveName
-
A descriptive-name must be exactly equal to (case-sensitive) this string.
- setErodeAtBoundary(boolean) - Method in class ConvexHullBase
-
- setError(int, Exception) - Method in class ResultsVector
-
Set an error state at a particular position.
- setErrorAll(Exception) - Method in class ResultsVector
-
Set an error state at all positions.
- setErrorDisconnectedObjects(boolean) - Method in class RemoveIntersectingVoxels
-
If true, throws an error if there is a disconnected object after the erosion
- setErrorTree(DefaultTreeModel) - Method in class ProposerFailureDescription
-
- setExactDepth(int) - Method in class DirectoryDepth
-
- setExceptionIfEmpty(boolean) - Method in class FeatureHistogramStatistic
-
If true, then an exception is thrown if the histogram is empty, otherwise
is returned.
- setExcludeZero(boolean) - Method in class Intensity
-
Iff true, zero-valued voxels are excluded from the histogram
- setExcludeZero(boolean) - Method in class IntensityMeanMaxSlice
-
- setExcludeZero(boolean) - Method in class Intensity
-
If true, zeros are excluded from considering in the histogram
- setExecutionTime(long) - Method in class OptimizationStep
-
- setExitBeforeOptimization(boolean) - Method in class SegmentWithMarkedPointProcess
-
Iff true the algorithm exits before optimization begins (useful for debugging).
- setExitWithMinima(boolean) - Method in class WatershedYeong
-
If true, exits early and just returns the minima, without any further segmentation
- setExpandLabelZ(boolean) - Method in class TileWithLabels
-
- setExperiment(RootedExperiment) - Method in class ExperimentResultsExperimentStructure
-
- setExperiment(RootedExperiment) - Method in class ExperimentStructure
-
- setExperimentIdentifier(ExperimentIdentifier) - Method in class OutputExperiment
-
A name for the experiment.
- setExperimentType(String) - Method in class FilePathAppendBase
-
A folder identifying the type of experiment (where the outputs are all put in the same
directory
- setExperimentType(String) - Method in class QuickMultiDatasetStructuredExperiment
-
The value of $1 (see comment above) in naming-structure.
- setExperimentType(String) - Method in class RootedExperiment
-
A directory identifying the type of experiment.
- setExpression(String) - Method in class RegExSimple
-
A Java-style regular expression containing groups.
- setExpression(String) - Method in class MatchRegularExpression
-
- setExpression(String) - Method in class RegularExpression
-
- setExtendInZ(boolean) - Method in class ExportObjectsAsCroppedImages
-
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all
slices)
- setExtension(String) - Method in class OneOrThreeChannelsWriter
-
- setExtension(String) - Method in class AppendStack
-
- setExtension(String) - Method in class AppendStackDirect
-
- setExtensions(StringSet) - Method in class MatchExtensions
-
A set of file-extensions (without the period), one of which must match the end of a path.
- setExtensions(StringSet) - Method in class BranchExtension
-
Any extensions to match (case insensitive) not including any leading period.
- setExtractScoreSize(ExtractScoreSize<S>) - Method in class DirectAssignMode
-
- setExtractScoreSize(ExtractScoreSize<S>) - Method in class UniformProposal
-
- setExtractScoreSizeReport(ExtractScoreSize<S>) - Method in class TransformationAssignMode
-
- setExtractScoreSizeState(ExtractScoreSize<T>) - Method in class TransformationAssignMode
-
- setExtractWeight(ExtractWeightFromMark) - Method in class KernelInitialMarksFromPartition
-
- setExtraLength(int) - Method in class Midpoint
-
- setFactor(double) - Method in class ScoreObjects
-
- setFactor(double) - Method in class Scale
-
- setFactorHigh(double) - Method in class Identity
-
- setFactorLow(double) - Method in class Identity
-
- setFactorStandardDeviation(double) - Method in class GaussianSampler
-
Multiples the standard deviation of the distribution found in keyStandardDeviation.
- setFallback(FilesProvider) - Method in class SpecificPathList
-
If no paths can be found either from listPaths or the input-context, then the fallback is
called if exists, otherwise an error is thrown
- setFallback(ScaleCalculator) - Method in class ToSuggested
-
- setFallback(ChannelConvertStyle) - Method in class RGB
-
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
- setFallback(ImageMetadataReader) - Method in class InferFromHeader
-
Fallback to use if EXIF information is non-existing or absent.
- setFallbackName(String) - Method in class ExperimentIdentifierAuto
-
If there's no task-name, then this constant is used as a fallback name
- setFeature(Feature<T>) - Method in class FeatureProviderDefine
-
The feature to provide.
- setFeature(Feature<T>) - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session.
- setFeature(FeatureListEvaluator<FeatureInputSingleObject>) - Method in class OutputFeatureTable
-
A list of features to calculate in an evaluation context.
- setFeature(Feature<FeatureInputSingleObject>) - Method in class ScoreObjects
-
Feature that calculates the score for an object.
- setFeature(Feature<T>) - Method in class PermuteFeatureBase
-
- setFeature(Feature<FeatureInputPairMemo>) - Method in class AddCriteriaFeatureRelationThreshold
-
- setFeature(FeatureProvider<T>) - Method in class FeatureValueCheckMark
-
- setFeature(FeatureProvider<FeatureInputMark>) - Method in class RequireFeatureRelationThreshold
-
- setFeatureCondition(Feature<T>) - Method in class IfCondition
-
- setFeatureCondition(Feature<T>) - Method in class IfConditionWithinRange
-
Calculates value for the condition - which is checked if it lies within a certain range
- setFeatureElse(Feature<T>) - Method in class IfCondition
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class MultipleComparer
-
Calculates the cost used when making assignments.
- setFeatureEvaluator(FeatureEvaluator<T>) - Method in class ReportFeatureEvaluator
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class FeatureCostAssigner
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class DiscardOutliers
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class RelationWithMatches
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class ThresholdedFeature
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class ObjectCollectionProviderWithFeature
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class MergeGreedyToIncreaseObjectFeature
-
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class MergeToIncreaseObjectFeature
-
- setFeatureEvaluatorMatch(FeatureEvaluator<FeatureInputSingleObject>) - Method in class RelationWithMatches
-
- setFeatureEvaluatorMerge(FeatureEvaluator<FeatureInputPairObjects>) - Method in class MergePairs
-
- setFeatureEvaluatorThreshold(FeatureEvaluator<FeatureInputNull>) - Method in class MergePairs
-
Allows merge only if the feature-value satisfies a relation to this threshold
- setFeatureProvider(FeatureProvider<T>) - Method in class FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session
- setFeatures(List<FeatureProvider<T>>) - Method in class FeatureListEvaluator
-
A list of providers, combined together to form a list of features, to be calculated in a
session
- setFeatures(List<NamedBean<FeatureListProvider<U>>>) - Method in class ExportFeatures
-
The features to be exported (after possibly some manipulation or augmentation).
- setFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>) - Method in class SegmentInstanceWithModel
-
Features to calculate for objects in the features output.
- setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>>) - Method in class ExportFeatures
-
- setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class PairNeighbors
-
Additional features that only depend on the image, so do not need to be replicated for every
object.
- setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>>) - Method in class PairNeighbors
-
Additional features that are processed on the pair of images (i.e.
- setFeatureTables(List<OutputFeatureTable>) - Method in class Develop
-
Specifies a feature-table that can also be outputted.
- setFeedbackReceiver(FeedbackReceiverBean<T>) - Method in class FeedbackReceiverRequireArguments
-
- setFeedbackReceiver(FeedbackReceiverBean<VoxelizedMarksWithEnergy>) - Method in class SegmentWithMarkedPointProcess
-
Processes feedback from the segmentation algorithm for outputting / debugging.
- setFileFilter(String) - Method in class ExperimentResultsExperimentStructure
-
Files to search for
- setFileFilterAndDirectory(Path) - Method in class SearchDirectory
-
Sets both the directory and the glob from a string containing both.
- setFileId(String) - Method in class AppendCsv
-
Unique identifier for the stack, object-mask-collection etc.
- setFileId(String) - Method in class FilePathBaseAppendToManagerWithFileID
-
Unique identifier for the stack, object-mask-collection etc.
- setFileInput(NamedFiles) - Method in class GroupFiles
-
- setFileInput(InputManager<FileInput>) - Method in class NamedChannels
-
- setFileInput(InputManager<FileInput>) - Method in class Stacks
-
- setFileInput(String) - Method in class QuickExperiment
-
A string indicating the input file(s)
- setFileName(String) - Method in class ReportFeatureForManifestFileBase
-
- setFilePath(String) - Method in class SortedSetSlice
-
- setFilePath(String) - Method in class FromSerializedMarks
-
- setFilePath(String) - Method in class FromSerializedObject
-
- setFilePathParser(FilePathParser) - Method in class MultiFileReader
-
- setFilePathProviderSVM(FilePathProvider) - Method in class FeatureListProviderSVMClassifier
-
- setFilePrefix(String) - Method in class MovieFromSlices
-
- setFiles(FilesProvider) - Method in class ReadFromFile
-
Provides a single file containing a dictionary.
- setFiles(FilesProvider) - Method in class FilesProviderUnary
-
- setFiles(FilesProviderWithDirectory) - Method in class FilesProviderWithDirectoryUnary
-
- setFiles(FilesProvider) - Method in class FromFiles
-
A provider that should return exactly one
File whose path is employed.
- setFiles(FilesProviderWithDirectory) - Method in class Rooted
-
- setFiles(FilesProvider) - Method in class NamedFiles
-
The files to use as inputs.
- setFiles(FilesProviderWithDirectory) - Method in class NamedFilesWithDirectory
-
The files to use as inputs.
- setFiles(FilesProviderWithDirectory) - Method in class QuickBase
-
A path to the main channel of each file
- setFilter(ObjectFilter) - Method in class IfObjectFilter
-
- setFilter(ObjectFilter) - Method in class ObjectCollectionProviderFilterBase
-
- setFilter(ObjectFilter) - Method in class Filter
-
- setFilter(ImageLabeller<T>) - Method in class ImageLabellerStringMap
-
- setFilterFilesCsv(MatchedAppendCsv) - Method in class QuickBase
-
If set, a CSV is read with two columns: the names of images and a
- setFindMaxima(boolean) - Method in class ExtractSlice
-
If true, the maxima of the score is searched for.
- setFindOutlinePixelAngle(FindPointOnContour) - Method in class TraversePointsOnContour
-
- setFirst(StringSet) - Method in class OutputEnableRulesSpecify
-
Output-names in the first-level.
- setFirst(boolean) - Method in class AsSingle
-
Iff true, first object is used, otherwise the second
- setFirst(StateTransformerBean<S, U>) - Method in class Compose
-
First transformation from S to U
- setFirstLineHeaders(boolean) - Method in class CombineCSV
-
- setFixRandomSeed(boolean) - Method in class SegmentWithMarkedPointProcess
-
Iff true uses a constant seed for the random-number-generator (useful for debugging).
- setFlatten(boolean) - Method in class MultipleComparer
-
If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane,
before comparison.
- setFlatten(boolean) - Method in class CompareAnnotations
-
If true, a maximum-intensity-projection is first applied to any 3D objects into a 2D plane,
before comparison.
- setFlatten(boolean) - Method in class ExteriorContour
-
If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make
it 2D
- setFlatten(boolean) - Method in class ColoredBase
-
If true, objects and the background are flattened in the z dimension (via maximum intensity
projection), so that a 2D image is produced.
- setFontColor(RGBColorBean) - Method in class TextStyle
-
Font-color of drawn text
- setFontName(String) - Method in class TextStyle
-
Font-name of drawn text
- setFontSize(int) - Method in class TextStyle
-
Font-size of drawn text
- setForceChangeBytes(boolean) - Method in class Invert
-
If true, rather than modifying the binary-values (an index) bytes are modified in the buffer
to reflect the existing binary-values.
- setForceDetailedLogging(boolean) - Method in class OutputExperiment
-
Whether more detailed log-messages around each experiment occur.
- setForceEagerEvaluation(boolean) - Method in class NamedChannelsAppend
-
- setForceReader(String) - Method in class BioformatsReader
-
If non-empty forces usage of a particular bioformats plugin.
- setForceRGB(boolean) - Method in class ArrangeRaster
-
If set, ensures every stack is converted into 3 channels
- setFormats(List<HeaderFormat>) - Method in class InferFromHeader
-
The formats whose headers will be searched, to find sufficient metadata to populate
ImageMetadata.
- setForwardDirectionOnly(boolean) - Method in class XYOrientationExtendToZ
-
- setFrom3i(ObjectMask) - Static method in class PointsFromObject
-
A sorted-set of three-dimensional integer points from the entire object-mask
- setFromContour(ObjectMask) - Static method in class PointsFromObject
-
A set of points from the contour of object in three dimensions.
- setGaussian(boolean) - Method in class AddEdgeFilters
-
If true, the Gaussian filter is included
- setGaussianSigmaMeters(double) - Method in class AddEdgeFilters
-
- setGeneratorList(List<RasterGenerator<T>>) - Method in class CombineRasterGenerator
-
- setGlob(String) - Method in class MatchGlob
-
The string describing a glob e.g.
- setGradient(ChannelProvider) - Method in class ScoreVoxels
-
- setGraphColorScheme(PlotColorScheme) - Method in class PlotIndexBase
-
- setGrayscaleReconstruction(GrayscaleReconstructionByErosion) - Method in class MinimaImpositionGrayscaleReconstruction
-
- setGreen(int) - Method in class RGBColorBean
-
Sets the green component value.
- setGreen(int) - Method in class RGBColor
-
Sets the green component value.
- setGreen(ChannelProvider) - Method in class ThreeChannels
-
- setGroup(String) - Method in class AnnotationLabel
-
Specifies a group for the label (similar labels that are displayed together)
- setGroup(DerivePath) - Method in class ExportFeatures
-
If non-null, this file-path is used to determine the group of the file.
- setGroup(DerivePath) - Method in class GroupedStackBase
-
If defined, translates a file-path into a group.
- setGroup(String) - Method in class CSVRow
-
- setGroup(String) - Method in class AppendHistogram
-
- setGroupNum(int) - Method in class RootFilePathRegEx
-
- setHeight(int) - Method in class SizeXY
-
Size in Y dimension.
- setHeight(double) - Method in class ImposeResolution
-
Physical pixel size of a voxel in y-dimension.
- setHighestTwoRadiiOnly(boolean) - Method in class RadiiRatio
-
- setHistogram(HistogramProvider) - Method in class HistogramProviderUnary
-
- setHistogram(HistogramProvider) - Method in class ConvertWithHistogram
-
If set, a histogram used in conversion to describe input intensities (across perhaps multiple
images).
- setHistogram(HistogramProvider) - Method in class SegmentChannel
-
An optional histogram of voxel intensity values which can be used by segment
- setHistogram(HistogramProvider) - Method in class PlotHistogram
-
The histogram to plot.
- setHistogram(HistogramProvider) - Method in class FromHistogram
-
If non-null, a histogram is extracted from this provider rather than the histogram from the
inputted CSV.
- setHistogramChannelIndex(int) - Method in class CalculateLevelBase
-
- setHistogramIndex(int) - Method in class IdentityImposeValueRelationToHistogram
-
- setHistogramsExtra(List<HistogramProvider>) - Method in class ScoreVoxels
-
- setHorizontalAlign(String) - Method in class Overlay
-
- setId(String) - Method in class DictionaryProviderReference
-
- setId(String) - Method in class Reference
-
The identifier that uniquely determines the other feature to reference.
- setId(String) - Method in class FeatureProviderReference
-
The name of the feature to reference.
- setId(String) - Method in class FeatureResultsStatistic
-
The name of the feature, whose results will provide the statistic.
- setId(String) - Method in class BinarySegmentationReference
-
- setId(String) - Method in class FilePathProviderReference
-
- setId(int) - Method in class Mark
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class FromChannel
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class ReferenceOrElse
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class FeatureIntersectingObjects
-
ID for the particular object-collection
- setId(DerivePath) - Method in class ExportFeatures
-
Translates an input file name to a unique ID.
- setId(String) - Method in class MarkBoundsReference
-
- setId(String) - Method in class MarkProposerReference
-
- setId(String) - Method in class MarkMergeProposerReference
-
- setId(String) - Method in class MarkSplitProposerReference
-
- setId(String) - Method in class Reference
-
- setId(String) - Method in class ReferenceOrEmpty
-
- setId(int) - Method in class CreateEllipse
-
- setId(String) - Method in class CSVRow
-
- setId(String) - Method in class Reference
-
- setIdentifierSubrange(Optional<IndexRangeNegative>) - Method in class InputContextParameters
-
If defined, this indicates and specifies only a subset of the naming-elements to use.
- setIdentifierSuffix(String) - Method in class QuickMultiDatasetExperiment
-
- setIdentifierSuffix(String) - Method in class QuickMultiDatasetStructuredExperiment
-
- setIdGenerator(DerivePath) - Method in class ExportObjectsFromCSV
-
- setIgnoreAtThreshold(boolean) - Method in class OutlineKernelBase
-
- setIgnoreCase(boolean) - Method in class FilePathPattern
-
if true, case is ignored in the pattern matching.
- setIgnoreContains(String) - Method in class AnnotationBackground
-
If non-empty, to not display any stacks in backgroundStackMap whose name contains
this string.
- setIgnoreFileNotFoundAppend(boolean) - Method in class NamedChannelsAppend
-
- setIgnoreFittingFailure(boolean) - Method in class FitPointsFromObjects
-
If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply
not included (with only a log error) If false, an exception is thrown
- setIgnoreHidden(boolean) - Method in class SearchDirectory
-
If true, case is ignored in the pattern matching.
- setIgnoreHidden(boolean) - Method in class FilePathPattern
-
Iff true, any hidden-path is not considered, and simply ignored
- setIgnoreHigherSide(boolean) - Method in class GaussianCumulative
-
- setIgnoreLowerSide(boolean) - Method in class GaussianCumulative
-
- setIgnoreMissingChannel(boolean) - Method in class IndependentChannels
-
Iff true and we cannot find a channel in the file, we ignore it and carry on
- setIgnoreNaN(boolean) - Method in class Sum
-
If true, we ignore any NaN values.
- setIgnoreNoObjects(boolean) - Method in class SegmentInstanceWithModel
-
If true, then the outputs (outline, mask, image etc.) are not written for images that produce
no objects.
- setIgnoreRangeAxisOutside(boolean) - Method in class LinePlot
-
- setIgnoreZero(boolean) - Method in class RatioNonMode
-
- setIgnoreZeros(boolean) - Method in class HistogramCSVGenerator
-
Iff true bins in the histogram with a zero count are not written
- setIgnoreZIfNaN(boolean) - Method in class DistanceTransform3D
-
If the z-resolution is undefined, the z dimenion is ignored.
- setImageLabeller(ImageLabeller<T>) - Method in class ImageAssignLabel
-
Maps a label to an image
- setImageMetadataReader(ImageMetadataReader) - Method in class ConvertNamedChannels
-
- setImgChannelMapCreator(ChannelMap) - Method in class GroupFiles
-
- setIncludeBatchDimension(boolean) - Method in class SegmentObjectsFromONNXModel
-
If true, a 4-dimensional tensor is created (with the first dimension describing a batch-size
of 1), instead of the usual 3-dimensional tensor describing channel, height, width.
- setIncludeDirectories(boolean) - Method in class DirectoryStructure
-
If false, the folders are ignored, and only the file-name is used in the output
- setIncludeFeatureNames(boolean) - Method in class EnergySchemeCreatorByElement
-
If true, the names of the imageFeatures are taken as a combination of the namedItem and the
actual features
- setIncludeFileName(boolean) - Method in class AppendDictionary
-
- setIncludeFirst(boolean) - Method in class PairNeighbors
-
Include features for the First-object of the pair
- setIncludeMerged(boolean) - Method in class PairNeighbors
-
Include features for the Merged-object of the pair
- setIncludeSecond(boolean) - Method in class PairNeighbors
-
Include features for the Second-object of the pair
- setIncludeShell(boolean) - Method in class MaxOverlapRatio
-
- setIncludeZ(boolean) - Method in class Outline
-
If true the outline is also applied in the z-dimension, otherwise this is ignored as possible
boundary
- setIncludeZ(boolean) - Method in class NotTouchingSceneBorder
-
- setIncrement(int) - Method in class SequenceInteger
-
Size of step to use when incrementing.
- setIndex(int) - Method in class ChannelEntry
-
- setIndex(int) - Method in class KernelPointCursor
-
The index in the buffer that the kernel currently is focussed on.
- setIndex(int) - Method in class AtIndex
-
- setIndex(int) - Method in class SliceAt
-
Index in z-dimension of slice to extract
- setIndex(int) - Method in class SpecificAxisBase
-
Specifies which principal-axis to use for calculations (0=largest eigenvalue,
1=second-largest eigenvalue etc.)
- setIndex(int) - Method in class IndexedRegionBase
-
- setIndex(int) - Method in class OrderedRadius
-
- setIndex(int) - Method in class AsObject
-
- setIndex(int) - Method in class HOGFeature
-
Which index to return from the HOG descriptor.
- setIndex(int, double) - Method in class DirectionVector
-
Sets an element of the vector by the index of its position.
- setIndexDay(int) - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the day, starting
from 0 for the first group.
- setIndexEnd(int) - Method in class ExtractSliceRange
-
Slice index to end extracting from (inclusive).
- setIndexHours(int) - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the hours, starting
from 0 for the first group.
- setIndexMinutes(int) - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the minutes, starting
from 0 for the first group.
- setIndexMonth(int) - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the month, starting
from 0 for the first group.
- setIndexNonZero(int) - Method in class SelectSlicesWithIndexBase
-
- setIndexSeconds(int) - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the seconds, starting
from 0 for the first group.
- setIndexStart(int) - Method in class ExtractSliceRange
-
Slice index to start extracting from (inclusive).
- setIndexYear(int) - Method in class TimestampPattern
-
The index of the group in regularExpression that encodes the year, starting
from 0 for the first group.
- setInitContext(OptimizationContext) - Method in class FeedbackBeginParameters
-
- setInitialKernel(Kernel<T, S>) - Method in class KernelProposer
-
- setInnerCoreDistance(double) - Method in class Ellipsoid
-
- setInput(InputManager<T>) - Method in class AnnotationInputManager
-
The inputs to be annotated.
- setInput(InputManager<T>) - Method in class InputOutputExperiment
-
The input-manager to specify where/which/how necessary inputs for the experiment occur.
- setInput(InputManager<T>) - Method in class InputManagerUnary
-
The delegate input-manager which will be circumstantially called by the current
input-manager.
- setInput(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor
-
- setInput(InputManager<? extends ProvidesStackInput>) - Method in class MultiInputManager
-
- setInput(InputManager<T>) - Method in class AnnotationComparisonInputManager
-
- setInput(InputManager<NamedChannelsInputPart>) - Method in class NamedChannelsAppend
-
- setInput(InputManager<NamedChannelsInput>) - Method in class ConvertNamedChannelsToStack
-
- setInput(MultiInputManager) - Method in class FromCSVInputManager
-
- setInputDebug(InputManager<T>) - Method in class BranchIfDebug
-
If defined, this provides an input to the manager when in debug-mode, rather than than
otherwise inputs.
- setInputDirectory(Optional<Path>) - Method in class InputContextParameters
-
If defined, a directory which can be used by beans to find input.
- setInputFilterExtensions(Set<String>) - Method in class InputContextParameters
-
A list of extensions that can be used filter inputs
- setInputFilterGlob(String) - Method in class InputContextParameters
-
A glob that can be used by beans to filter input
- setInputName(String) - Method in class MultiInputManager
-
- setInputName(String) - Method in class SegmentObjectsFromONNXModel
-
The name of the input in the ONNX model.
- setInputName(String) - Method in class QuickExperiment
-
- setInputName(String) - Method in class MultiInputManagerQuick
-
- setInputPaths(Optional<List<Path>>) - Method in class InputContextParameters
-
A list of paths referring to specific inputs
- setInputPointShift(float) - Method in class ConicFitterBase
-
- setIntensity(ChannelProvider) - Method in class ScoreVoxels
-
- setIntensityProvider(Provider<Stack>) - Method in class GenerateString
-
- setInterleaveChannels(boolean) - Method in class SegmentObjectsFromONNXModel
-
If true, the channels are placed as the final position of the tensor (**after** width/height)
instead of **before** width/height.
- setInterpolate(boolean) - Method in class AtScale
-
- setInterpolator(InterpolatorBean) - Method in class ScaleXY
-
- setInterpolator(InterpolatorBean) - Method in class OutlinePreserveRelativeSize
-
Interpolator used when scaling the background
- setInterpolator(InterpolatorBean) - Method in class ScaleToSize
-
- setInverse(boolean) - Method in class IntersectsWithContainer
-
- setInverse(boolean) - Method in class IntensityMeanShellBase
-
Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is
removed).
- setInverseMask(boolean) - Method in class IntensityMeanShellBase
-
If true, uses the inverse of the passed mask.
- setInvert(boolean) - Method in class MaskAsObject
-
- setInvert(boolean) - Method in class FromObjects
-
- setInvert(boolean) - Method in class FilterWithRegularExpression
-
Iff true, then a file is rejected if the regular-expression matches and vice-versa.
- setInvertDecisionValue(boolean) - Method in class FeatureListProviderSVMClassifier
-
- setItem(T) - Method in class NamedBean
-
The item that is to be named, the underlying bean.
- setItem(Feature<T>) - Method in class DefineSingle
-
The sole feature that forms the list.
- setItem(FeatureListProvider<FeatureInput>) - Method in class PrependName
-
Provides the features and names before any prepending.
- setItem(Feature<S>) - Method in class FeatureUnary
-
- setItem(Feature<FeatureInputSingleObject>) - Method in class FeatureDeriveFromPair
-
- setItem(ReportFeature<MarksInitialization>) - Method in class ReportFeatureWrapError
-
- setItem(Feature<FeatureInputHistogram>) - Method in class ThresholdHistogram
-
- setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class DeriveFromPair
-
- setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class FeatureListProviderAggregatePair
-
For each feature in the list, a corresponding aggregate feature is created in the
output list.
- setItem(Feature<FeatureInputHistogram>) - Method in class Intensity
-
Feature to apply to the histogram
- setItem(Feature<FeatureInputSingleObject>) - Method in class DerivedObject
-
- setItem(Feature<FeatureInputPairObjects>) - Method in class FeatureIntersectingObjectsSingleElement
-
- setItem(FeaturePairObjects) - Method in class PairedWithMask
-
- setItem(VoxelScore) - Method in class RejectIfIntensityLessThan
-
- setItem(Feature<FeatureInputSingleObject>) - Method in class FeatureSingleObjectFromShared
-
- setItem(Feature<FeatureInputHistogram>) - Method in class Intensity
-
Feature to apply to the histogram
- setItem(Feature<FeatureInputSingleObject>) - Method in class AsObjectMask
-
- setItem(Feature<FeatureInputSingleObject>) - Method in class QuantileAcrossConnectedComponents
-
- setItem(DerivePath) - Method in class Rooted
-
- setItem(Feature<FeatureInputSingleMemo>) - Method in class CoefficientOfVarianceFromAll
-
- setItem(Feature<FeatureInputSingleMemo>) - Method in class MeanFromAll
-
- setItem(Feature<FeatureInputHistogram>) - Method in class Intensity
-
Feature to apply to the histogram
- setItem(Feature<FeatureInputSingleMemo>) - Method in class FeaturePairMemoOne
-
- setItem1(Feature<T>) - Method in class FeatureBinary
-
Provides the first value for the binary-function.
- setItem2(Feature<T>) - Method in class FeatureBinary
-
Provides the second value for the binary-function.
- setItemMean(Feature<T>) - Method in class StatisticalBase
-
- setItemProportionate(Feature<FeatureInputSingleMemo>) - Method in class FeatureAsIndividualProportionate
-
- setItemStdDev(Feature<T>) - Method in class StatisticalBase
-
- setIterations(int) - Method in class AnisotropicDiffusion
-
How many iterations to perform diffusion.
- setIterations(int) - Method in class MorphologicalOperatorBase
-
- setIterations(int) - Method in class ObjectCollectionProviderMorphological
-
- setIterations(int) - Method in class Repeat
-
The maximum number of iterations.
- setIterations(MorphologicalIterations) - Method in class Intersection
-
The number of dilations and erosions to apply to determine if two objects intersect
- setIterations(MorphologicalIterations) - Method in class IntensityMeanShellBase
-
The number of dilations and erosions to apply and whether to do in the Z dimension.
- setIterations(int) - Method in class Erode
-
- setIterations(int) - Method in class NumberRemovedVoxelsAfterClosing
-
- setIterations(MorphologicalIterations) - Method in class Shell
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- setIterations(int) - Method in class MorphologicalOperation
-
iterations for erode, dilate, open, close
- setIterations(int) - Method in class UniformProposal
-
- setIterations(int) - Method in class NumberIterationsBase
-
The number of iterations for which the number-of-marks must remain constant.
- setIterationsDilation(int) - Method in class MorphologicalIterations
-
Number of times to perform morphological dilation
- setIterationsErosion(int) - Method in class MorphologicalIterations
-
Number of times to perform morphological erosion
- setJobNumber(int) - Method in class JobDescription
-
- setJobShortName(String) - Method in class JobDescription
-
- setKappa(double) - Method in class AnisotropicDiffusion
-
A parameter kappa associated with the diffusion functions.
- setKeepEntireImage(boolean) - Method in class ExportObjectsAsCroppedImages
-
If true, rather than writing out a bounding-box around the object-mask, the entire image is
written
- setKeepExtremes(boolean) - Method in class Identity
-
- setKeepProcessorsFree(int) - Method in class DebugDependentProcessor
-
How many processors to avoid using for the tasks.
- setKeepProcessorsFree(int) - Method in class ParallelProcessor
-
How many processors to avoid using for the tasks.
- setKeepZ(boolean) - Method in class ImposeResolution
-
Keep the z-resolution if it is already defined
- setKernel(Kernel<T, S>) - Method in class WeightedKernel
-
- setKernel(Kernel<T, S>) - Method in class KernelProposerOptionSingle
-
- setKernelFactoryList(WeightedKernelList<?, ?>) - Method in class FeedbackBeginParameters
-
- setKernelHalfWidth(int) - Method in class Median
-
Kernel will be a square kernel of size (2*kernelHalfWidth+1)x(2*kernelHalfWidth+1)
- setKernelNegative(KernelPosNeg<T, S>) - Method in class KernelProposerOptionDual
-
- setKernelPositive(KernelPosNeg<T, S>) - Method in class KernelProposerOptionDual
-
- setKernelProposer(KernelProposer<VoxelizedMarksWithEnergy, UpdatableMarksList>) - Method in class SegmentWithMarkedPointProcess
-
Proposes kernel-changes during iterations of hte marked-point-processes.
- setKernelStateBridge(KernelStateBridge<U, T>) - Method in class TransformationAssignMode
-
- setKey(String) - Method in class AssignFromDictionary
-
The key of the value in the dictionary that will be assigned.
- setKey(String) - Method in class DictionaryCondition
-
The key in the dictionary whose value is checked.
- setKey(String) - Method in class IfParamEqual
-
- setKey(String) - Method in class ParamFromCollection
-
The name of the key in the dictionary, whose corresponding value will be returned.
- setKey(String) - Method in class FromDictionary
-
- setKeyGroupID(int) - Method in class RegularExpression
-
- setKeyLower(String) - Method in class ScaleByDictionary
-
- setKeyMean(String) - Method in class GaussianSampler
-
The name of the key in the dictionary with the mean of the distribution.
- setKeyPrefix(String) - Method in class FromDictionary
-
Prefix prepended to key
- setKeyRequired(boolean) - Method in class RegularExpression
-
- setKeyStandardDeviation(String) - Method in class GaussianSampler
-
The name of the key in the dictionary with the standard-deviation.
- setKeySuffix(String) - Method in class FromDictionary
-
- setKeyUpper(String) - Method in class ScaleByDictionary
-
- setLabel(String) - Method in class StackProviderWithLabel
-
- setLabel(boolean) - Method in class MontageSlices
-
If true a label is added beside every image showing the slice index
- setLabels(List<AnnotationLabel>) - Method in class ImageLabelStrategy
-
- setLevel(int) - Method in class Constant
-
- setLine(String[]) - Method in class CSVRow
-
- setList(List<DefineAdderBean>) - Method in class Concatenate
-
- setList(List<RegEx>) - Method in class RegExList
-
The list of
RegExes that are successively tried to be matched.
- setList(List<StringMapItem>) - Method in class StringMap
-
A list of mappings between a single-items in the respective sets.
- setList(List<LoggingDestination>) - Method in class ToMultiple
-
The list of loggers to log to
- setList(List<Feature<T>>) - Method in class Define
-
The list that specifies features.
- setList(List<NamedBean<FeatureListProvider<T>>>) - Method in class DefinedNamed
-
- setList(List<Feature<T>>) - Method in class FeatureList
-
The list of features.
- setList(List<Feature<T>>) - Method in class FeatureFromList
-
Assigns the list of features to use.
- setList(FeatureList<T>) - Method in class FeatureFromList
-
Assigns the list of features to use.
- setList(List<Provider<Stack>>) - Method in class ArrangeRaster
-
- setList(List<DrawObject>) - Method in class Combine
-
- setList(List<StackProviderWithLabel>) - Method in class TileWithLabels
-
- setList(List<RegionMembership>) - Method in class RegionMap
-
- setList(List<AddCriteriaPair>) - Method in class AddCriteriaOr
-
- setList(List<FeedbackReceiver<T>>) - Method in class FeedbackReceiverList
-
- setList(List<TerminationCondition>) - Method in class TerminationConditionListOr
-
- setList(List<ColorProvider>) - Method in class Concatenate
-
- setList(List<CalculateLevel>) - Method in class CalculateLevelListBase
-
- setList(List<ObjectFilter>) - Method in class ObjectFilterCombine
-
A list of other filters from which the sub-classes implement filtering behaviour.
- setList(List<ObjectCollectionProvider>) - Method in class Concatenate
-
- setList(List<BinarySegmentation>) - Method in class Sequence
-
A list of binary-segmentations that are applied successively (the output of the predecessor
becomes the input of the sucecssor)
- setList(List<ProviderAsStack>) - Method in class Concatenate
-
- setList(List<NamedBean<FromStack>>) - Method in class SpecificAndRename
-
- setList(List<ChannelEntry>) - Method in class FromEntries
-
- setList(List<FilesProvider>) - Method in class Combine
-
- setList(List<InputManager<T>>) - Method in class Concatenate
-
- setList(List<Summarizer<T>>) - Method in class SummarizerAggregate
-
- setList(List<CheckMark>) - Method in class AndList
-
- setList(List<VisitScheduler>) - Method in class VisitSchedulerAnd
-
- setList(List<VisitScheduler>) - Method in class VisitSchedulerUniformSample
-
- setList(List<MarkProposer>) - Method in class MarkProposerFromList
-
- setListAdditionalChannelProviders(List<ChannelProvider>) - Method in class ScoreObjects
-
- setListAppend(List<NamedBean<DerivePath>>) - Method in class NamedChannelsAppend
-
- setListAppend(List<FilePathBaseAppendToManager>) - Method in class MultiInputManagerQuick
-
Additional entities that are appended to the multi-input
- setListFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class BinaryClassifierImageLabeller
-
- setListImageFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class EnergySchemeCreatorByElement
-
- setListPaths(StringList) - Method in class SpecificPathList
-
If specified, this forms the list of paths which is provided as input.
- setListReportFeatures(List<ReportFeature<U>>) - Method in class ExportReportFeatures
-
- setListStackProvider(List<NamedBean<StackProvider>>) - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- setListStackProviderMIP(List<NamedBean<StackProvider>>) - Method in class ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- setLocalized(boolean) - Method in class FilesProviderWithDirectoryString
-
- setLog(LoggingDestination) - Method in class OnlyIf
-
The logger to use if conditions are fulfilled
- setLogExperiment(LoggingDestination) - Method in class OutputExperiment
-
Where log messages that do not pertain to a specific job (input) appear.
- setLogExperimentPath(String) - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for the experiment in gneeral
- setLoggerTaskCreator(LoggingDestination) - Method in class ParametersExperiment
-
This is a means to create new log-reporters for each task.
- setLogPath(boolean) - Method in class Rooted
-
if true, the pathIn and pathOut are logged.
- setLogTask(LoggingDestination) - Method in class InputOutputExperiment
-
Where log messages that do pertain to a specific job (input) appear.
- setLogTaskPath(String) - Method in class QuickMultiDatasetExperiment
-
Relative path to a logger for a specific task
- setMainChannelIndex(int) - Method in class NamedChannelsQuick
-
Index of the mainChannel
- setMainChannelName(String) - Method in class NamedChannelsQuick
-
The name of the channel provided by the rasters in file Provider
- setManifestDescriptionFunction(String) - Method in class MarksGeneratorBase
-
- setManifestDeserializer(ManifestDeserializer) - Method in class CoupledManifestsInputManager
-
- setManifestExperimentInputFileSet(FilesProvider) - Method in class CoupledManifestsInputManager
-
- setManifestFunction(String) - Method in class ObjectSerializerPeriodicReporter
-
- setManifestFunction(String) - Method in class VoxelizedMarksChangeReporter
-
- setManifestInputFileSet(FilesProvider) - Method in class CoupledManifestsInputManager
-
- setMap(StringMap) - Method in class ImageLabellerStringMap
-
- setMarkBounds(MarkBounds) - Method in class MarkBoundsDefine
-
- setMarkBounds(MarkBounds) - Method in class SegmentThresholdAboveMinBound
-
- setMarkEvaluator(NamedBean<MarkEvaluator>) - Method in class MarkProposerStrategy
-
A mark-evaluator that is added to the GUI to support this annotation
- setMarkFactory(MarkWithIdentifierFactory) - Method in class MarkEvaluator
-
- setMarkFactory(MarkWithIdentifierFactory) - Method in class SegmentWithMarkedPointProcess
-
Creates a new mark, before perhaps further manipulations by a kernel.
- setMarkFactory(MarkFactory) - Method in class FitPointsFromObjects
-
- setMarkFromMarksProposer(MarkFromCollectionProposer) - Method in class KernelSplit
-
- setMarkProposer(String) - Method in class MarkProposerStrategy
-
- setMarkProposer(MarkProposer) - Method in class FromMarkProposer
-
- setMarkProposer(MarkProposer) - Method in class MergeMarkEllipse
-
- setMarkProposer(MarkProposer) - Method in class KernelBirthAndKill
-
- setMarkProposer(MarkProposer) - Method in class KernelExchange
-
- setMarkProposer(MarkProposer) - Method in class KernelBirthVoxelized
-
- setMarkProposerAdditionalBirth(MarkProposer) - Method in class KernelBirthAndKill
-
- setMarkProvider(SingleMarkProvider) - Method in class CreateMarkFromPoints
-
- setMarkProvider(SingleMarkProvider) - Method in class ReportFeatureOnMark
-
- setMarkProvider(SingleMarkProvider) - Method in class FromSingleMark
-
- setMarkProvider(Provider<Optional<Mark>>) - Method in class RequireFeatureRelationThreshold
-
- setMarks(MarkCollection) - Method in class MarksWithTotalEnergy
-
The marks
- setMarks(MarkCollectionProvider) - Method in class ReportFeatureOnMarks
-
- setMarks(MarkCollection) - Method in class MarksWithDisplayStack
-
- setMarks(Point2d, Orientation) - Method in class Ellipse
-
- setMarks(MarkCollectionProvider) - Method in class FromMarks
-
- setMarks(MarkCollectionProvider) - Method in class ScaleXY
-
- setMarks(MarkCollectionProvider) - Method in class RetrieveSingleMarkOnly
-
- setMarks(MarkCollectionProvider) - Method in class ColoredMarks
-
- setMarksColored(ColoredMarks) - Method in class ColoredMarksWithDisplayStack
-
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class ConicBase
-
- setMarksExplicit(Point3d, Orientation) - Method in class ConicBase
-
- setMarksExplicit(Point3d) - Method in class ConicBase
-
- setMarksExplicit(Point3d, Orientation, Point2d) - Method in class Ellipse
-
- setMarksExplicit(Point3d) - Method in class Ellipse
-
- setMarksExplicit(Point3d, Orientation) - Method in class Ellipse
-
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class Ellipse
-
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class Ellipsoid
-
- setMarksExplicit(Point3d) - Method in class Ellipsoid
-
- setMarksExplicit(Point3d, Orientation) - Method in class Ellipsoid
-
- setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksFromPartition
-
- setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksProposed
-
- setMarksProposer(MarkCollectionProposer) - Method in class KernelInitialMarksVoxelized
-
- setMask(Provider<Mask>) - Method in class MaskProviderUnary
-
- setMask(MaskProvider) - Method in class FromMaskBase
-
- setMask(MaskProvider) - Method in class UnaryWithMaskBase
-
- setMask(MaskProvider) - Method in class ScoreVoxels
-
- setMask(MaskProvider) - Method in class FromChannel
-
- setMask(MaskProvider) - Method in class SegmentChannel
-
An optional mask which restricts the algorithm to only parts of the channel where the mask
has an on voxel
- setMask(Provider<Mask>) - Method in class ConnectedComponentsFromMask
-
- setMask(MaskProvider) - Method in class AndObjectsWithMasks
-
- setMask(Provider<Mask>) - Method in class FromMask
-
- setMask(MaskProvider) - Method in class SegmentChannel
-
- setMask(MaskProvider) - Method in class ColoredMask
-
- setMask(Provider<Mask>) - Method in class FromChannelOrMask
-
A mask that is provided to the stack.
- setMask(MaskProvider) - Method in class PairedWithMask
-
- setMask(MaskProvider) - Method in class MaskAsSingleObject
-
- setMask(MaskProvider) - Method in class FillHoles
-
- setMask(Provider<Mask>) - Method in class CheckMarkWithMask
-
- setMask(Provider<Mask>) - Method in class FindPointOnContourWalk
-
- setMask(Provider<Mask>) - Method in class XYOrientationExtendToZ
-
- setMaskContour(Provider<Mask>) - Method in class TraverseOuterContourOnImage
-
- setMaskElse(MaskProvider) - Method in class IfPredicateBase
-
Returned instead of mask if the predicate is not satisfied
- setMaskFilled(Provider<Mask>) - Method in class TraverseOuterContourOnImage
-
- setMaskFilled(Provider<Mask>) - Method in class XYOrientationExtendToZ
-
- setMaskIndex(int) - Method in class SurfaceSizeMaskNonZero
-
- setMaskValue(int) - Method in class ExportImageHistograms
-
What voxel value to read as "On" in the mask above.
- setMaskValue(int) - Method in class OverlapMaskBase
-
- setMatch(String) - Method in class FilterCSVColumn
-
- setMatch(String) - Method in class MatchedAppendCsv
-
- setMatcher(PathMatcher) - Method in class SearchDirectory
-
- setMatcher(PathMatcher) - Method in class MatchExtensions
-
- setMatcher(ObjectMatcher) - Method in class RelationWithMatches
-
- setMatcher(ObjectMatcher) - Method in class ObjectWithMaximumFeatureFromEachMatchedCollection
-
- setMatcher(ObjectMatcher) - Method in class Match
-
- setMax(int) - Method in interface Progress
-
Assigns the maximum value of progress that is possible.
- setMax(int) - Method in class ProgressConsole
-
- setMax(int) - Method in class ProgressIgnore
-
- setMax(int) - Method in class ProgressIncrement
-
Assigns the maximum value of progress that is possible.
- setMax(double) - Method in class BoundMinMax
-
- setMax(double) - Method in class ResolvedBound
-
- setMax(int) - Method in class ScaleByMinMaxValue
-
- setMax(int) - Method in class ClampHistogramMax
-
- setMax(UnitValueAreaOrVolume) - Method in class UnitsWithinRange
-
Maximum-boundary for acceptable range
- setMax(boolean) - Method in class IdentityImposeValueRelationToHistogram
-
- setMax(int) - Method in class OutsideRange
-
- setMax(double) - Method in class MaxOverlapRatio
-
- setMax(double) - Method in class InvertedMax
-
- setMax(Feature<T>) - Method in class CompareWithRangeFeature
-
Calculates maximally-allowed range boundary
- setMax(double) - Method in class RangeCompareFromScalars
-
Boundary value indicating maximally-allowed range value
- setMaxCost(double) - Method in class MultipleComparer
-
The maximum cost (as calculated by featureEvaluator) to accept when creating an
assignment between objects.
- setMaxCost(double) - Method in class FeatureCostAssigner
-
- setMaxDirectoryDepth(int) - Method in class SearchDirectory
-
If non-negative the max depth of directories.
- setMaxDirectoryDepth(int) - Method in class ExperimentResultsExperimentStructure
-
- setMaxDistance(UnitValueDistance) - Method in class MergeWithOptionalDistanceConstraint
-
An optional maximum distance
- setMaxDistance(UnitValueDistance) - Method in class CostOverlapWithinMidpointDistance
-
- setMaxDistance(UnitValueDistance) - Method in class FindPointOnContourWalk
-
- setMaxDistanceBetweenMinima(UnitValueDistance) - Method in class AddDistanceTransform
-
- setMaxDistanceCOG(UnitValueDistance) - Method in class MergeSpatialClusters
-
The maximum distance allowed between center-of-gravities of objects
- setMaxDistanceDeltaContour(double) - Method in class AddDistanceTransform
-
The maximum distance allowed between two seeds in terms of their values in the distance map
- setMaxDistanceDeltaContour(double) - Method in class MergeSpatialClusters
-
The maximum distance allowed between the 'distance from contour' values provided from the
distanceMap for each point.
- setMaxDistanceProposer(ScalarProposer) - Method in class VisitSchedulerMaxDistanceAlongContour
-
- setMaxDistanceZ(ScalarProposer) - Method in class XYOrientationExtendToZ
-
- setMaximumNumberChannels(int) - Method in class IntensityMoments
-
An upper limit on the number of channels in the energy-stack for which we create features.
- setMaxIter(int) - Method in class Repeat
-
- setMaxIter(int) - Method in class Repeat
-
- setMaxIter(int) - Method in class Repeat
-
- setMaxIter(int) - Method in class RadiiProposerRepeat
-
- setMaxNumberItems(int) - Method in class Limit
-
- setMaxNumberItems(int) - Method in class Limit
-
- setMaxNumberProcessors(int) - Method in class DebugDependentProcessor
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- setMaxNumberProcessors(int) - Method in class ParallelProcessor
-
Theoretical maximum number of (CPU) processors to use in parallel.
- setMaxNumberProcessors(int) - Method in class QuickMultiDatasetExperiment
-
An upper limit on the number of the processors that can be simultaneously used in parallel,
if they are available.
- setMaxNumberProcessors(int) - Method in class QuickMultiDatasetStructuredExperiment
-
- setMaxNumItems(int) - Method in class LimitWithDirectory
-
- setMaxSize(long) - Method in class Mser
-
- setMaxSplitGroups(int) - Method in class CompareAnnotations
-
- setMaxValue(long) - Method in class ToByteScaleByMaxValue
-
Assigns the maximum-value that will be represented in the scaled-values.
- setMaxVar(double) - Method in class Mser
-
- setMaxVolume(UnitValueAreaOrVolume) - Method in class FillHoles
-
- setMaxX(int) - Method in class Box
-
Maximum X coordinate inclusive.
- setMaxY(int) - Method in class Box
-
Maximum Y coordinate inclusive.
- setMaxZ(int) - Method in class Box
-
Maximum Z coordinate inclusive.
- setMean(double) - Method in class MeanScale
-
The mean.
- setMedian(boolean) - Method in class AddEdgeFilters
-
If true, the median filter is included
- setMedianRadiusMeters(double) - Method in class AddEdgeFilters
-
- setMerge(boolean) - Method in class CutBelowThreshold
-
- setMergedPosTolerance(double) - Method in class MergeMarkEllipse
-
- setMergeMarkProposer(MarkMergeProposer) - Method in class KernelMerge
-
- setMessage(String) - Method in class ReportFeatureWrapError
-
- setMessageNoInputs(String) - Method in class InputOutputExperiment
-
A message written to the logger if no inputs exist for the experiment, and it thus ends
early.
- setMethod(String) - Method in class AutoLocalThreshold
-
- setMethod(String) - Method in class ThresholderAutoIJ
-
One of the following strings to identify ImageJ's thresholding algorithms (or an empty string
for the default).
- setMethod(CopyFilesMethod) - Method in class CopyFiles
-
How the copying occurs from source to destination file.
- setMin(int) - Method in interface Progress
-
Assigns the minimum value of progress that is possible.
- setMin(int) - Method in class ProgressConsole
-
- setMin(int) - Method in class ProgressIgnore
-
- setMin(int) - Method in class ProgressIncrement
-
Assigns the minimum value of progress that is possible.
- setMin(double) - Method in class BoundMinMax
-
- setMin(double) - Method in class ResolvedBound
-
- setMin(int) - Method in class ScaleByMinMaxValue
-
- setMin(UnitValueAreaOrVolume) - Method in class UnitsWithinRange
-
Minimum-boundary for acceptable range
- setMin(int) - Method in class OutsideRange
-
- setMin(double) - Method in class RadiiMinRatio
-
- setMin(Feature<T>) - Method in class CompareWithRangeFeature
-
Calculates minimally-allowed range boundary
- setMin(double) - Method in class RangeCompareFromScalars
-
Boundary value indicating minimally-allowed range value
- setMinConfidence(double) - Method in class ThresholdConfidence
-
The minimum confidence of an element for its object-mask to be initially included for
consideration (before merging).
- setMinConfidence(float) - Method in class DecodeMaskRCNN
-
Only proposals outputted from the model with a score greater or equal to this threshold are
considered.
- setMinConfidence(double) - Method in class DecodeEAST
-
Proposed bounding boxes below this confidence interval are removed from consideration.
- setMinDiff(double) - Method in class MeanIntensityDifference
-
- setMinDifference(int) - Method in class Difference
-
A minimum difference, below which 0.0 is returned
- setMinDifference(int) - Method in class DifferenceCalculateLevelStandardDeviation
-
- setMinDiversity(double) - Method in class Mser
-
- setMinimaImposition(MinimaImposition) - Method in class ImposeMinima
-
- setMinimumBoundingBoxVolume(int) - Method in class FloodFillEachIntensityLevel
-
Only objects whose bounding-box volume is greater or equal to this threshold are included.
- setMinimumPerCluster(int) - Method in class ClusterByTimestamp
-
The minimum number of files that must exist for a cluster.
- setMinIntensity(int) - Method in class RejectIfIntensityLessThan
-
- setMinIntensity(int) - Method in class ThresholderSimpleFillHoles2D
-
Intensity for thresholding
- setMinIntensityValue(int) - Method in class MorphologicalOperatorBase
-
- setMinMaskValue(float) - Method in class DecodeMaskRCNN
-
Only voxels with a value greater or equal to this threshold are considered as part of the
mask.
- setMinMaxIgnoreBeforeIndex(int) - Method in class LinePlot
-
- setMinMaxValues(int, int) - Method in class ToByteScaleByMinMaxValue
-
Assigns the minimum- and maximum-values which existing values are scaled against.
- setMinNumberObjects(int) - Method in class DiscardOutliers
-
- setMinNumberPoints(int) - Method in class SplitContourAtSaddlePoints
-
If a contour has less than this number of points, we don't split it, and return it as-is
- setMinNumberVoxels(int) - Method in class SplitIntoSquares
-
Only includes squares that have at least this number of voxels.
- setMinNumberVoxels(int) - Method in class ConnectedComponentsFromBinarySegmentation
-
- setMinNumberVoxels(int) - Method in class ThresholdConfidence
-
The minimum number of voxels that must exist in a connected-component to be included.
- setMinNumPoints(int) - Method in class CreateMarkFromPoints
-
- setMinNumPoints(int) - Method in class PointsFitterToMark
-
If an object has fewer points than before being fitted, we ignore
- setMinNumSlices(int) - Method in class XYOrientationExtendToZ
-
- setMinNumZSlices(int) - Method in class AtLeastZSlices
-
- setMinOverlap(double) - Method in class CostOverlapWithinMidpointDistance
-
- setMinRadius(double) - Method in class LinearLeastSquaresEllipseFitter
-
- setMinRadius(double) - Method in class LinearLeastSquaresEllipsoidFitter
-
- setMinRatio(double) - Method in class DiscardOutliers
-
- setMinResolution(double) - Method in class MinimumXYResolution
-
- setMinSize(long) - Method in class Mser
-
- setMinVal(double) - Method in class FeatureValueCheckMark
-
- setMinVolume(UnitValueAreaOrVolume) - Method in class ConnectedComponentsFromMask
-
- setMinVolume(UnitValueVolume) - Method in class VolumeMin
-
- setMinVolumeConnectedComponent(UnitValueVolume) - Method in class AddDistanceTransform
-
- setMinX(int) - Method in class Box
-
Minimum X coordinate inclusive.
- setMinY(int) - Method in class Box
-
Minimum Y coordinate inclusive.
- setMinZ(int) - Method in class Box
-
Minimum Z coordinate inclusive.
- setMip(boolean) - Method in class NumberVoxels
-
- setMip(boolean) - Method in class SurfaceNumberVoxelsBase
-
- setMip(boolean) - Method in class OverlapMIPBase
-
- setModelBinaryPath(String) - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb extension, relative
to the models/ directory in the Anchor distribution.
- setModelPath(String) - Method in class SegmentObjectsFromONNXModel
-
Relative-path to the model file in ONNX form, relative to the models/ directory in the
Anchor distribution.
- setModelTextGraphPath(String) - Method in class SegmentObjectsFromTensorFlowModel
-
Relative-path to the TensorFlow model file, likely with .pb.txt extension,
relative to the models/ directory in the Anchor distribution.
- setMultipleComparer(MultipleComparer) - Method in class MarkProposerStrategy
-
- setMultipleOf(int) - Method in class FitTo
-
The eventual width and height of the image must be a multiple of this number.
- setMultiplyBy(float) - Method in class DistanceTransform3D
-
- setName(String) - Method in class FromXMLList
-
The name of the file in the current working directory WITHOUT THE .xml EXTENSION
- setName(String) - Method in class NamedBean
-
The name associated with item.
- setName(String) - Method in class RootPath
-
The name of the root-path, which need not be unique in itself.
- setName(String) - Method in interface NameValue
-
Assigns the associated name.
- setName(String) - Method in class SimpleNameValue
-
- setName(String) - Method in class ExperimentIdentifierConstant
-
- setName(String) - Method in class ChannelEntry
-
- setName(String) - Method in class Kernel
-
- setName(String) - Method in class WeightedKernel
-
- setName(String) - Method in class AdjacentFile
-
A name to describe the adjacent file
- setName(String) - Method in class FilePathAppendBase
-
The name of the appended entity
- setNameLeft(String) - Method in class AnnotationComparisonInputManager
-
- setNamer(FileNamer) - Method in class GroupFiles
-
- setNamer(FileNamer) - Method in class RemoveExtension
-
- setNamer(FileNamer) - Method in class SubsetRangeIfRequested
-
The namer that is called to provide names that are subsetted.
- setNamer(FileNamer) - Method in class NamedFilesBase
-
- setNamer(FileNamer) - Method in class QuickBase
-
Assigns each input a unique compact name.
- setNameRight(String) - Method in class AnnotationComparisonInputManager
-
- setNaming(CopyFilesNaming<T>) - Method in class CopyFiles
-
How an output name (and path) is selected for an input file.
- setNavigateHigherDirectories(int) - Method in class MultiFileReader
-
Search x number directories higher than file.
- setNoBlack(boolean) - Method in class ThresholderAutoIJ
-
- setNormalize(boolean) - Method in class Identity
-
- setNormalize(boolean) - Method in class BoundingBoxZOverlapRatio
-
- setNormalizeFeatures(boolean) - Method in class FeatureListProviderSVMClassifier
-
Normalize features
- setNumberBins(int) - Method in class HOGParameters
-
The number of bins in each histogram for a cell.
- setNumberChannels(int) - Method in class ForceNumberChannels
-
- setNumberColors(int) - Method in class TiffTimeSeries
-
- setNumberColumns(int) - Method in class Tile
-
The number of columns to use in the table produced when tiling.
- setNumberColumns(int) - Method in class CSVReader.OpenedCSVFile
-
- setNumberDecimalPlaces(int) - Method in class FeatureCostAssigner
-
- setNumberDigits(int) - Method in class IncrementingNumber
-
Number of digits in the number, with leading zeros as necessary.
- setNumberDilations(int) - Method in class LevelPerObjectIndependently
-
- setNumberFrames(int) - Method in class ForceNumberFrames
-
- setNumberGPUProcessors(int) - Method in class ParallelProcessor
-
How many GPU processors to use when this is possible as a substitute for a CPU processor
- setNumberLevelsGrouping(int) - Method in class CompareAnnotations
-
- setNumberLoopPoints(int) - Method in class SplitContourAtSaddlePoints
-
- setNumberPoints(int) - Method in class LinePlot
-
- setNumberRows(int) - Method in class Tile
-
The number of rows to use in the table produced when tiling.
- setNumberSubdirectories(int) - Method in class LastDirectories
-
How many directories to include in the name.
- setNumCols(int) - Method in class TileWithLabels
-
- setNumMarks(int) - Method in class FromMarkProposer
-
- setObjectMatcher(ObjectMatcher) - Method in class Bridge
-
Used to match each intermediary-object to a final-object
- setObjects(Provider<ObjectCollection>) - Method in class ObjectCollectionProviderUnary
-
- setObjects(ObjectCollectionProvider) - Method in class OutputFeatureTable
-
The objects for which features are calculated.
- setObjects(ObjectCollectionProvider) - Method in class ReportFeatureOnObjectsBase
-
- setObjects(ObjectCollectionProvider) - Method in class DistanceTransformForEachObject3D
-
- setObjects(ObjectCollectionProvider) - Method in class LevelPerObjectBase
-
The objects for whom a level is calculated
- setObjects(ObjectCollectionProvider) - Method in class UnaryWithObjectsBase
-
- setObjects(ObjectCollectionProvider) - Method in class GenerateToMatchObjects
-
- setObjects(ObjectCollectionProvider) - Method in class FromObjects
-
- setObjects(ObjectCollectionProvider) - Method in class IntersectsWith
-
- setObjects(ObjectCollectionProvider) - Method in class Always
-
- setObjects(ObjectCollectionProvider) - Method in class Intersection
-
- setObjects(ObjectCollectionProvider) - Method in class Permute
-
- setObjects(ObjectCollectionProvider) - Method in class ColoredObjects
-
Objects to draw on a background
- setObjects(ObjectCollectionProvider) - Method in class ObjectAggregationBase
-
- setObjects(ObjectCollectionProvider) - Method in class FromObjects
-
- setObjects(ObjectCollectionProvider) - Method in class ObjectAsPoints
-
- setObjects(ObjectCollectionProvider) - Method in class IncludeRandomObjects
-
- setObjects(ObjectCollectionProvider) - Method in class PointsFromObjects
-
- setObjects(List<NamedBean<ObjectCollectionProvider>>) - Method in class FromObjects
-
- setObjects(ObjectCollectionProvider) - Method in class ExportObjectsBase
-
- setObjects(ObjectCollectionProvider) - Method in class PointsFitterToMark
-
- setObjects1(ObjectCollectionProvider) - Method in class MergeTwoCollectionsItemwise
-
First collection with items to be merged
- setObjects2(ObjectCollectionProvider) - Method in class MergeTwoCollectionsItemwise
-
Second collection with items to be merged
- setObjectsBlue(ObjectCollectionProvider) - Method in class ThreeColoredObjects
-
- setObjectsContainer(ObjectCollectionProvider) - Method in class WithContainerBase
-
- setObjectsElse(ObjectCollectionProvider) - Method in class ReferenceOrElse
-
- setObjectsGreater(ObjectCollectionProvider) - Method in class GreaterIntersectionWith
-
- setObjectsGreen(ObjectCollectionProvider) - Method in class ThreeColoredObjects
-
- setObjectsGrouped(ObjectCollectionProvider) - Method in class FilterByGroup
-
- setObjectsLesser(ObjectCollectionProvider) - Method in class GreaterIntersectionWith
-
- setObjectsRed(ObjectCollectionProvider) - Method in class ThreeColoredObjects
-
- setObjectsRejected(ObjectCollectionProvider) - Method in class ObjectCollectionProviderFilterBase
-
- setObjectsSeeds(ObjectCollectionProvider) - Method in class SegmentChannel
-
- setObjectsSeeds(ObjectCollectionProvider) - Method in class SegmentWithSeeds
-
- setObjectsSource(ObjectCollectionProvider) - Method in class AssignFromIntersectingObjects
-
- setObjectsSource(ObjectCollectionProvider) - Method in class SegmentWithSeeds
-
- setObjectsSplitBy(ObjectCollectionProvider) - Method in class SplitByObjects
-
- setObjectsTarget(ObjectCollectionProvider) - Method in class AssignFromIntersectingObjects
-
- setOfConnectedComponentIDs() - Method in class EncodedVoxels
-
- setOff(int, int, int) - Method in interface BinaryOnOffSetter
-
Assigns an off state to a voxel at a particular point.
- setOff(Point3i) - Method in interface BinaryOnOffSetter
-
Assigns an off state to a voxel at a particular point.
- setOn(int, int, int) - Method in interface BinaryOnOffSetter
-
Assigns an on state to a voxel at a particular point.
- setOn(Point3i) - Method in interface BinaryOnOffSetter
-
Assigns an on state to a voxel at a particular point.
- setOpenInDesktop(boolean) - Method in class ExperimentExecutor
-
Whether to open the output directory in the desktop GUI after execution (if supported on the
O/S).
- SetOperationFailedException - Exception in org.anchoranalysis.core.index
-
When a set operation fails for a particular key.
- SetOperationFailedException(String) - Constructor for exception SetOperationFailedException
-
Creates with only a message.
- SetOperationFailedException(Throwable) - Constructor for exception SetOperationFailedException
-
Creates with only a cause.
- setOptimization(OptimizationScheme<VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy, UpdatableMarksList>) - Method in class SegmentWithMarkedPointProcess
-
The optimization-scheme that determines which configurations are accepted/rejected from one
iteration to the next.
- setOptionList(List<KernelProposerOption<T, S>>) - Method in class KernelProposer
-
- setOptions(ReadOptions) - Method in class BioformatsReader
-
Options that influence how stack is read.
- setOptions(ReadOptions) - Method in class ReadOptionsDelegate
-
- setOrientationProposer(OrientationProposer) - Method in class OrientationAndRadiiProposer
-
- setOrientationXYProposer(OrientationProposer) - Method in class XYOrientationExtendToZ
-
- setOtherwise(FileNamer) - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is not selected.
- setOutline(boolean) - Method in class ColoredBase
-
If true, an outline is drawn around the entries.
- setOutlineAtBoundary(boolean) - Method in class ExteriorContour
-
- setOutlineColor(RGBColorBean) - Method in class SegmentInstanceWithModel
-
The color of the outline.
- setOutlinePixelsRetriever(TraverseOuterCounter) - Method in class TraversePointsOnContour
-
- setOutlinePixelsRetrieverReverse(TraverseOuterCounter) - Method in class TraversePointsOnContour
-
- setOutlineWidth(int) - Method in class BoundingBoxOutline
-
- setOutlineWidth(int) - Method in class Outline
-
- setOutlineWidth(int) - Method in class CompareAnnotations
-
How many pixels should the outline be around objects.
- setOutlineWidth(int) - Method in class AtScale
-
- setOutlineWidth(int) - Method in class ColoredBase
-
The width of the outline (only relevant if outline==true.
- setOutlineWidth(int) - Method in class OutlinePreserveRelativeSize
-
The width of the outline.
- setOutlineWidth(int) - Method in class SegmentInstanceWithModel
-
The width of the outline.
- setOutlineWidth(int) - Method in class VisualizeOnBackground
-
- setOutlineWidth(int) - Method in class ExportObjectsAsCroppedImages
-
- setOutPath(String) - Method in class InsertRegExGroups
-
Constructs a path as an output, replacing $1, $2 etc.
- setOutput(OutputManager) - Method in class OutputExperiment
-
The output-manager that specifies how/where/which elements occur duing outputting.
- setOutput(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor
-
- setOutput(String) - Method in class QuickMultiDatasetExperiment
-
- setOutputName(String) - Method in class ToTextFileBase
-
The name to use (without extension) for the text-file log
- setOutputName(String) - Method in class OutputNameStyle
-
An identifier used in rules to determine if an output is enabled or not.
- setOutputName(String) - Method in class PeriodicSubdirectoryReporter
-
- setOutputName(String) - Method in class MinimalExecutionTimeStatsReporter
-
- setOutputName(String) - Method in class VoxelizedMarksChangeReporter
-
- setOutputNameStyle(IndexableOutputNameStyle) - Method in class FromOutputName
-
- setOutputRGBOutline(StringSet) - Method in class ExportObjectsAsCroppedImages
-
- setOutputRGBOutlineFlattened(StringSet) - Method in class ExportObjectsAsCroppedImages
-
- setOutputsDisabled(StringSet) - Method in class SpecificDisabled
-
The names of the outputs that are disbled.
- setOutputsEnabled(StringSet) - Method in class SpecificEnabled
-
The names of the outputs that are enabled.
- setOutputsEnabled(OutputEnabledRules) - Method in class OutputManager
-
Which outputs are enabled or not enabled.
- setOutputShort(boolean) - Method in class GradientBase
-
Iff true, outputs a short channel, otherwise byte channel
- setOutputStackProvider(StackProvider) - Method in class ImageAssignLabel
-
If it's set, a stack is generated that is outputted into subdirectory corresponding to the
groupIdentifier.
- setOutputWriteSettings(OutputWriteSettings) - Method in class OutputManager
-
General settings (default file extensions, colors etc.) for outtping files.
- setOutputWriteSettings(OutputWriteSettings) - Method in class QuickExperiment
-
- setOutside(double) - Method in class UnitsWithinRange
-
Returned as a constant if a value lies otside the range
- setOutsideAtThreshold(boolean) - Method in class OutlineKernelBase
-
- setOverlappingObjects(boolean) - Method in class OutlinePreserveRelativeSize
-
Whether objects may overlap or not when unscaled.
- setOverlapRatioThreshold(double) - Method in class KernelBirthAndKill
-
- setPadding(double) - Method in class TextStyle
-
Padding added around the text in both dimensions if a default size is inferred (ignored if an
explicit size is specified )
- setPadding(Padding) - Method in class DrawCroppedObjectsGenerator
-
- setPadding(Padding) - Method in class ExportObjectsBase
-
Padding placed on each side of the outputted image (if it's within the image)
- setPaddingXY(int) - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in XY
directions
- setPaddingZ(int) - Method in class Padding
-
Padding placed on each side of the outputted image (if it's within the image) in Z direction
- setPairAddCriteria(AddCriteriaPair) - Method in class EnergySchemeCreatorByElement
-
- setPairCollection(RandomCollection<IdentifiablePair<Mark>>) - Method in class KernelMerge
-
- setPairTypeClass(Class<?>) - Method in class RandomCollectionWithAddCriteria
-
- setParam(P) - Method in class BeanInitializer
-
Sets the current parameters used for propagation.
- setParameters(Dictionary) - Method in class EnergyStack
-
The associated parameters.
- setParameters(HOGParameters) - Method in class HOGDescriptor
-
Parameters used for calculating HOG
- setParameters(HOGParameters) - Method in class HOGFeature
-
Parameters used for calculating HOG.
- setParamPrefix(String) - Method in class PermuteFeatureSequenceInteger
-
- setParamPrefixAppendNumber(boolean) - Method in class PermuteFirstSecondOrder
-
If true the constant is appended to the param prefix (a dot and a number)
- setPath(String) - Method in class RootPath
-
A path on a file-system to the directory, that defines the root.
- setPath(String) - Method in class SingleFile
-
- setPath(String) - Method in class RootedFilePath
-
- setPath(String) - Method in class StaticFilePath
-
- setPathAnnotation(DerivePath) - Method in class SinglePathStrategy
-
Derives the path to the corresponding annotation files, given a path to the image to be
annotated.
- setPathDefaultMarks(DerivePath) - Method in class MarkProposerStrategy
-
- setPathDictionary(DerivePath) - Method in class MarkProposerStrategy
-
- setPathLabel(DerivePath) - Method in class ImageCSVLabeller
-
Path to a CSV label file (comma-separated, with header, no quotes)
- setPathParser(FilePathParser) - Method in class GroupFiles
-
- setPaths(StringSet) - Method in class FileSetFromStringSet
-
- setPaths(List<DerivePath>) - Method in class FilterForExistingFiles
-
All files need to be present
- setPenaltyValue(double) - Method in class MaxOverlapRatio
-
- setPeriodTriggerBank(PeriodTriggerBank<T>) - Method in class FeedbackBeginParameters
-
- setPermutation(PermuteProperty<S>) - Method in class PermuteFeature
-
A permutation to apply.
- setPermutations(List<PermuteProperty<S>>) - Method in class PermuteFeature
-
A list of permutations to apply.
- setPermuteProperty(PermuteProperty<?>) - Method in class Permute
-
- setPermuteProperty(PermutePropertySequenceInteger) - Method in class PermuteFeatureSequenceInteger
-
- setPhysical(boolean) - Method in class UnitConverter
-
- setPlotBackgroundColor(RGBColorBean) - Method in class PlotColorScheme
-
- setPlotGridlineColor(RGBColorBean) - Method in class PlotColorScheme
-
- setPoint(Point3i, int) - Method in class EncodedVoxels
-
- setPointConnectedComponentID(Point3i, int) - Method in class EncodedVoxels
-
- setPointDirection(Point3i, int, int, int) - Method in class EncodedVoxels
-
- setPoints(Point3i, Point3i) - Method in class LineSegment
-
- setPoints(Point3d, Point3d) - Method in class LineSegment
-
- setPointsFitter(PointsFitter) - Method in class CreateMarkFromPoints
-
- setPointsFitter(String) - Method in class MarkProposerStrategy
-
- setPointsFitter(PointsFitter) - Method in class FitPoints
-
- setPointsFitter(PointsFitterToMark) - Method in class FitPointsFromObjects
-
- setPointsFitter(PointsFitter) - Method in class PointsFitterToMark
-
- setPointsFitter(PointsFitter) - Method in class ReflectInAxesWithinDistance
-
- setPointsFromOrientationProposer(PointsFromOrientationProposer) - Method in class MergeLists
-
- setPointsFromOrientationXYProposer(PointsFromOrientationProposer) - Method in class XYOrientationExtendToZ
-
- setPointsProposer(PointsProposer) - Method in class FitPoints
-
- setPosition(Point3d) - Method in class MarkWithPosition
-
- setPositionProposer(PositionProposer) - Method in class Position
-
- setPositionProposer(PositionProposer) - Method in class Repeat
-
- setPower(double) - Method in class MeanRaisedToPower
-
- setPrefix(String) - Method in class DefineAdderWithPrefixBean
-
A prefix that is placed before the name of every bean created.
- setPrefix(boolean) - Method in class FromXMLList
-
If true, a prefix is prepended to the name of each added bean.
- setPrefix(String) - Method in class PrependName
-
The string to prepend to the custom-name of each feature.
- setPrefix(String) - Method in class PathPrefixerAvoidResolve
-
A string prefixed to each output-path.
- setPrefix(String) - Method in class DirectoryWithPrefix
-
Always prepended to outputted filenames.
- setPrefix(String) - Method in class DeriveFromPair
-
- setPrefix(String) - Method in class FeatureListProviderAggregatePair
-
The string to prepend.
- setPrefix(String) - Method in class ExperimentStructure
-
- setPrefixer(PathPrefixer) - Method in class OutputManager
-
Determines a prefix to use when outputting a file based upon an input-path.
- setPrefixer(PathPrefixerAvoidResolve) - Method in class LastDirectoryAsPrefix
-
- setPrefixer(PathPrefixerAvoidResolve) - Method in class Rooted
-
- setPrefixerElse(PathPrefixerAvoidResolve) - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is not true.
- setPrefixerIf(PathPrefixerAvoidResolve) - Method in class IfIncrementingNumberRequested
-
Called if the requested condition is true.
- setPrefixToRemove(String) - Method in class DirectoryStructure
-
- setPrependColor(RGBColorBean) - Method in class Prepend
-
The color to prepend.
- setPreserveAspectRatio(boolean) - Method in class FitTo
-
If true, the aspect-ratio is preserved between width and height.
- setPreserveAspectRatio(boolean) - Method in class ToDimensions
-
If true, the ratio between x and y is kept constant when scaling.
- setPreserveExtensionIfDuplicate(boolean) - Method in class RemoveExtension
-
Keeps the extension if the file-name (without the extension) becomes duplicated with another.
- setPreserveSubdirectories(boolean) - Method in class ClusterByTimestamp
-
If true, the entire relative-path is used when copying files into the cluster directory.
- setPrioritizeInputContext(boolean) - Method in class MatchExtensions
-
When true, any extensions available in the input-context are prioritized ahead of extensions.
- setProbNeg(double) - Method in class KernelPosNeg
-
- setProbPos(double) - Method in class KernelPosNeg
-
- setProperty(String, T) - Method in class ObjectWithProperties
-
Assigns a value to a property with a particular name.
- setPropertyPath(String) - Method in class PermuteProperty
-
Either a direct property of a bean or a nested-property with the children separated by
full-stops.
- setProposal(boolean) - Method in class VoxelizedMarksPeriodicReporter
-
- setProposer(MarkFromCollectionProposer) - Method in class MarkFromCollectionProposerUnary
-
- setProposer(MarkProposer) - Method in class MarkProposerUnary
-
- setProvider(MarkCollectionProvider) - Method in class FromProvider
-
- setPxlPartMemo(EnergyMemoList) - Method in class FeatureInputAllMemo
-
- setPxlPartMemo(VoxelizedMarkMemo) - Method in class FeatureInputSingleMemo
-
- setQuantile(double) - Method in class Quantile
-
The quantile.
- setQuantile(double) - Method in class QuantileStretch
-
- setQuantile(double) - Method in class Quantile
-
- setQuantile(double) - Method in class DiscardOutliers
-
- setQuantile(double) - Method in class Quantile
-
- setQuantile(double) - Method in class QuantileAcrossObjects
-
- setQuantile(double) - Method in class QuantileAcrossConnectedComponents
-
- setQuantileHigh(double) - Method in class Range
-
- setQuantileLow(double) - Method in class Range
-
- setQuantileLower(double) - Method in class ToByteUpperLowerQuantileIntensity
-
- setQuantileUpper(double) - Method in class ToByteUpperLowerQuantileIntensity
-
- setRadiiProposer(RadiiProposer) - Method in class OrientationAndRadiiProposer
-
- setRadiiProposer(RadiiProposer) - Method in class RadiiProposerRepeat
-
- setRadius(double) - Method in class MarkWithPositionAndSingleRadius
-
- setRadius(int) - Method in class AutoLocalThreshold
-
- setRadius(double) - Method in class WithRadiusBase
-
- setRadiusBound(Bound) - Method in class UniformRandomRadiiProposer
-
- setRadiusInMeters(boolean) - Method in class WithRadiusBase
-
- setRadiusX(double) - Method in class FitResult
-
- setRadiusY(double) - Method in class FitResult
-
- setRadiusZ(double) - Method in class FitResult
-
- setRate(double) - Method in class Geometry
-
- setReader(StackReaderOrientationCorrection) - Method in class RotateImageToMatchEXIFOrientation
-
Reads the image that is subsequently flattened.
- setReaderMatching(StackReader) - Method in class BranchExtension
-
The reader to use if the extension matches.
- setReaderNotMatching(StackReader) - Method in class BranchExtension
-
The reader to use if the extension does not match.
- setReadFromResources(boolean) - Method in class SegmentObjectsFromONNXModel
-
When true, rather than reading modelPath from the file-system, it is read from Java
resources on the class-path.
- setReceive(MaskProvider) - Method in class CombineBase
-
- setRecurseSubfolders(boolean) - Method in class MultiFileReader
-
- setRecursive(boolean) - Method in class SearchDirectory
-
If true the search is applied recursively over sub-directories.
- setRecursive(boolean) - Method in class ExperimentResultsExperimentStructure
-
Whether to apply the search recursively or not
- setRed(int) - Method in class RGBColorBean
-
Sets the red component value.
- setRed(int) - Method in class RGBColor
-
Sets the red component value.
- setRed(ChannelProvider) - Method in class ThreeChannels
-
- setReduce(FeatureFromList<FeatureInputPairObjects>) - Method in class FeatureListProviderAggregatePair
-
Method for reducing all pairs into a single value e.g.
- setReferencePoissonIntensity(double) - Method in class MarkWithIdentifierFactory
-
- setReferences(StringSet) - Method in class ReferencingFeatureListProvider
-
The names of other feature-lists, whose features may be referenced by this feature.
- setReferencesFeatureListCreator(StringSet) - Method in class PermuteFeature
-
Makes sure a particular feature list creator is evaluated
- setReferencesList(String) - Method in class FeatureProviderReference
-
The name of the list in which the feature referenced by id resides.
- setRegex(String) - Method in class RegularExpressionBase
-
- setRegEx(RegEx) - Method in class RegExMatcher
-
- setRegEx(RegEx) - Method in class PathRegEx
-
Regular expression to use to match path with at least one group in it.
- setRegEx(RegEx) - Method in class RemoveMatching
-
If a path matches a regular expression it is removed.
- setRegEx(RegEx) - Method in class Exclude
-
A regular-expression to be matched against the identifiers of inputs.
- setRegEx(RegEx) - Method in class InsertRegExGroups
-
The regular-expression to use for matching groups.
- setRegEx(RegEx) - Method in class JoinRegExGroups
-
- setRegex(String) - Method in class Replace
-
Regular expression to match against string
- setRegex(String) - Method in class QuickBase
-
A regular-expression applied to the image file-path that matches three groups.
- setRegEx(RegEx) - Method in class ExperimentStructure
-
- setRegexAdjacent(String) - Method in class NamedChannelsQuick
-
This needs to be set if there is at least one adjacentChannel.
- setRegExDir(String) - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to directories.
- setRegExFile(String) - Method in class MultiFileReader
-
If non-empty a regular-expression is applied to files.
- setRegExString(String) - Method in class InsertRegExGroups
-
The regular-expression to use for matching groups, overloaded to handle legacy situations
where a string is supplied.
- setRegion(MarkRegion) - Method in class Thresholded
-
- setRegion(MarkRegion) - Method in class Intensity
-
- setRegionID(int) - Method in class VolumeMin
-
- setRegionID(int) - Method in class FromMarks
-
- setRegionID(int) - Method in class IndexedRegionBase
-
- setRegionID(int) - Method in class ColoredMarks
-
- setRegionID(int) - Method in class FeatureMarkRegion
-
- setRegionID(int) - Method in class FeatureSingleMemoRegion
-
- setRegionID(int) - Method in class FeaturePairMemoSingleRegion
-
- setRegionID(int) - Method in class KernelBirthAndKill
-
- setRegionMap(RegionMap) - Method in class EnergySchemeCreatorByElement
-
- setRegionMap(RegionMap) - Method in class FromMarks
-
- setRegionMap(RegionMap) - Method in class AsObject
-
- setRegionMap(RegionMap) - Method in class SurfaceSizeMaskNonZero
-
- setRegularExpression(String) - Method in class TimestampPattern
-
The regular-expression that checks a match and specifies groups for the encoded date-time.
- setRejectIterationIfAllLow(boolean) - Method in class Erode
-
- setRejectIterationIfDisconnected(boolean) - Method in class Erode
-
- setRelation(RelationBean) - Method in class RelationToConstant
-
The relation to the threshold, where the threshold forms the second operand.
- setRelation(RelationBean) - Method in class ObjectFilterRelation
-
- setRelation(RelationBean) - Method in class MergePairs
-
Relation to threshold
- setRelation(RelationBean) - Method in class IdentityImposeValueRelationToHistogram
-
- setRelation(RelationToThreshold) - Method in class RejectIfConditionXYResolution
-
A predicate defined by the relationship of the XY-resolution to a constant threshold.
- setRelation(RelationBean) - Method in class AddCriteriaFeatureRelationThreshold
-
- setRelation(RelationBean) - Method in class RequireFeatureRelationThreshold
-
- setRelativeForIdentifier(boolean) - Method in class InputContextParameters
-
If true, the entire filename or relative path (excluding extension) is used to determine a
unique identifier.
- setRemoveExtension(boolean) - Method in class FilePathPattern
-
if true, the extension is removed from paths before finding the pattern.
- setRemoveExtensionInDescription(boolean) - Method in class LastDirectories
-
Whether to remove the file-extension from the filename.
- setRemoveNaNColumns(boolean) - Method in class ExportFeaturesStyle
-
When true, columns containing all
Double.NaN values are removed before outputting.
- setRemoveTouchingBorderXY(boolean) - Method in class FeatureCostAssigner
-
- setRepeat(int) - Method in class MovieFromSlices
-
- setRepeats(int) - Method in class KernelBirth
-
Total number of births
- setRepeatZProvider(Provider<Stack>) - Method in class GenerateString
-
Repeats the generated (2D) string in z, so it's the same z-extent as repeatZProvider
- setReplaceMatchesWithSolids(boolean) - Method in class CompareAnnotations
-
- setReplacement(String) - Method in class SubstituteRegularExpression
-
- setReplacement(String) - Method in class Replace
-
What to replace in the path
- setReplacement(String) - Method in class AdjacentFile
-
The replacement string used to determine the file
- setReplaceWithMidpoint(boolean) - Method in class MergeGreedyToIncreaseObjectFeature
-
- setReportFitterErrors(boolean) - Method in class FitPoints
-
- setRequireAllFilesMatch(boolean) - Method in class GroupFiles
-
- setRequireArguments(RequireArguments) - Method in class OnlyIf
-
The conditions that must be fulfilled
- setRequireArguments(RequireArguments) - Method in class FeedbackReceiverRequireArguments
-
- setRequireBBoxNeighbors(boolean) - Method in class MergeWithFeature
-
Requires for any potential merge that the bounding-boxes of the two objects must intersect or
touch
- setRequireTouching(boolean) - Method in class MergeWithFeature
-
Requires the object-masks to touch.
- setResizeTo(SizeXY) - Method in class GroupedMeanChannelTask
-
If set, each channel is scaled to a specific size before the mean is calculated (useful for
combining different sized images)
- setResizeTo(SizeXY) - Method in class HOGDescriptor
-
The input-image is rescaled to this width/height before calculating HOG descriptors
- setResizeTo(SizeXY) - Method in class HOGFeature
-
The input is rescaled to this width/height before calculating HOG descriptors.
- setRestrictTo(MaskProvider) - Method in class Invert
-
If set, the inversion only occurs on a particular region of the mask, as determined by this
mask
- setRewardHigherSide(boolean) - Method in class GaussianCumulative
-
Treat the higher side as if it's the the fill cdf
- setRewardLowerSide(boolean) - Method in class GaussianCumulative
-
- setRgb(boolean) - Method in class FromChannelOrMask
-
If true, the output contains three channels (the input and two duplicates) instead of one
- setRoot1(double) - Method in class QuadraticEquationSolver.QuadraticRoots
-
The first root.
- setRoot2(double) - Method in class QuadraticEquationSolver.QuadraticRoots
-
The second root.
- setRootInStructure(boolean) - Method in class ExperimentResultsExperimentStructure
-
If true the directory structure is
ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory
structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
- setRootName(String) - Method in class Rooted
-
The name of the root-path to associate with this fileset.
- setRootName(String) - Method in class RootedFilePath
-
- setRootName(String) - Method in class Rooted
-
- setRootName(String) - Method in class Rooted
-
- setRootName(String) - Method in class QuickBase
-
If non-empty then a rooted filesystem is used with this root
- setRootName(String) - Method in class RootedExperiment
-
Root-name assuming multi-rooted structure.
- setRootNameForStructure(String) - Method in class ExperimentResultsExperimentStructure
-
If rootInStructure==true, the rootName is placed in the folder structure.
- setRootPath(Path) - Method in class RootDirectory
-
- setRotationAngle(Bound) - Method in class BoundRotation2D
-
- setRotationX(Bound) - Method in class BoundRotation3D
-
- setRotationY(Bound) - Method in class BoundRotation3D
-
- setRotationZ(Bound) - Method in class BoundRotation3D
-
- setRotMatrix(DoubleMatrix2D) - Method in class FitResult
-
The rotation matrix, which must be considered immutable to be used here.
- setRow(int) - Method in class Cell
-
- setSampleEvery(int) - Method in class SampleWithDirectory
-
- setScalarProposer(ScalarProposer) - Method in class MaxWithConstant
-
- setScalarProposer(ScalarProposer) - Method in class Scale
-
- setScale(double) - Method in class MeanScale
-
The scale, typically the standard-deviation.
- setScale(double) - Method in class MontageSlices
-
Whether to increase or reduce the size of the images
- setScaleCalculator(ScaleCalculator) - Method in class ScaleXY
-
- setScaleCalculator(ScaleCalculator) - Method in class ScaleXY
-
Determines how much to scale by
- setScaleCalculator(ScaleCalculator) - Method in class Scale
-
- setScaleCalculator(ScaleCalculator) - Method in class AtScale
-
- setScaleCalculator(ScaleCalculator) - Method in class Invert
-
- setScaleCalculator(ScaleCalculator) - Method in class ScaleImage
-
Calculates what scale-factor to apply on the image.
- setScaleCalculator(ScaleCalculator) - Method in class ScaleXY
-
- setScaleFactor(double) - Method in class GradientBase
-
- setScaleLabel(boolean) - Method in class TileWithLabels
-
- setScaleLower(double) - Method in class ScaleByDictionary
-
- setScaleLower(double) - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the min by multiplying the quantileLower by this constant.
- setScaleRadii(double) - Method in class ConicFitterBase
-
- setScaleUpper(double) - Method in class ScaleByDictionary
-
- setScaleUpper(double) - Method in class ToByteUpperLowerQuantileIntensity
-
Sets the max by multiplying the quantileUpper by this constant.
- setScore(VoxelScore) - Method in class ScoreVoxels
-
- setScoreProvider(FeatureListProvider<FeatureInputStack>) - Method in class ExtractSlice
-
- setSecond(boolean) - Method in class ExperimentIdentifierAuto
-
Only relevant if time==true.
- setSecond(List<NamedBean<StringSet>>) - Method in class OutputEnableRulesSpecify
-
Output-names in the second-level (for all first level output-names)
- setSecond(StateTransformerBean<U, T>) - Method in class Compose
-
Second transformation from U to T
- setSecondary(boolean) - Method in class VoxelizedMarksPeriodicReporter
-
If proposal is true, this toggles between the primary and secondary proposal
- setSecondary(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class StateReporterToPixelized
-
- setSegment(BinarySegmentation) - Method in class BinarySegmentationOne
-
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannelIntoObjectsUnary
-
- setSegment(BinarySegmentation) - Method in class SegmentChannel
-
Segmentation algorithm
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannel
-
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentChannelByObject
-
- setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class SegmentStack
-
The segmentation procedure.
- setSegment(SegmentChannelIntoObjects) - Method in class SegmentWithSeeds
-
- setSegment(BinarySegmentation) - Method in class ConnectedComponentsFromBinarySegmentation
-
- setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class SegmentInstanceWithModel
-
The segmentation algorithm.
- setSegment(SegmentIntoMarks) - Method in class SegmentMarksFromImage
-
How to perform the segmentation.
- setSegmentStack(BinarySegmentation) - Method in class SegmentOnMaximumIntensityAndExpandInZ
-
- setSelect(String) - Method in class DeriveFromPair
-
Either "merged" or "first" or "second" indicating which feature to delegate from
- setSelectChannels(FromStacks) - Method in class GroupedStackBase
-
Selects which channels are included, optionally renaming.
- setSeperator(String) - Method in class CombineCSV
-
- setSequence(SequenceInteger) - Method in class PermutePropertySequence
-
A sequence of integers, with each element assigned assigned directly during the permutation,
or after further manipulation.
- setSequence(OutputSequenceIndexed<T, S>) - Method in class ChangeableOutputSequence
-
- setSeriesIndex(int) - Method in class FromStackReader
-
The series to open to the read the metadata (zero-indexed).
- setSharedState(S) - Method in class SharedStateRememberConverted
-
The shared state.
- setShell(double) - Method in class MarkEllipseFactory
-
- setShell(double) - Method in class MarkEllipsoidFactory
-
- setShell(double) - Method in class Ellipse
-
The size of the shell, expressed as a ratio of the radius.
- setShell(double) - Method in class Ellipsoid
-
- setShell(double) - Method in class FromObjects
-
- setShell(double) - Method in class CreateEllipse
-
- setShell(double) - Method in class ConicFitterBase
-
- setShowAgg(boolean) - Method in class MemoryUsageReporter
-
- setShowBest(boolean) - Method in class MemoryUsageReporter
-
- setShowDomainAxis(boolean) - Method in class BarPlot
-
- setShowOngoingJobsLessThan(int) - Method in class ParallelProcessor
-
When the number of ongoing jobs is less than this threshold, they are shown in event logs.
- setShowVerticalAxisLines(boolean) - Method in class PlotInstance
-
- setShuffle(boolean) - Method in class InputContextParameters
-
If true, the order of the inputs are shuffled (randomized).
- setSigma(double) - Method in class BlurStrategy
-
- setSigma(double) - Method in class GaussianBlur2D
-
- setSigmaInMeters(boolean) - Method in class BlurStrategy
-
- setSilentlyDeleteExisting(boolean) - Method in class OutputManager
-
Whether to silently first delete any existing output at the intended path, or rather throw an
error.
- setSimplePairCollectionID(String) - Method in class KernelMerge
-
- setSize(SizeXY) - Method in class TextStyle
-
Explicit size of the image the string is draw on
- setSize(double) - Method in class Aggregator
-
- setSize(SizeXY) - Method in class PlotHistogram
-
Size of the image produced showing a plot of the histogram.
- setSize(SizeXY) - Method in class OutlinePreserveRelativeSize
-
Size of all created thumbnails
- setSize(SizeXY) - Method in class ScaleToSize
-
- setSize(SizeXY) - Method in class MovieFromSlices
-
- setSizeXY(SizeXY) - Method in class SpecifyDimensions
-
Length of X and Y dimensions.
- setSizeZ(int) - Method in class SpecifyDimensions
-
Length of Z dimension.
- setSkipAtBorder(boolean) - Method in class FillHoles
-
If true we do not fill any objects that touch the border
- setSkipFileName(boolean) - Method in class LastDirectories
-
Iff true the filename is not considered, only the subdirectories.
- setSkipFileName(boolean) - Method in class FilePathAppendBase
-
- setSkipFirstTrim(int) - Method in class RemoveTrailingDirectory
-
- setSkipFirstTrim(int) - Method in class FilePathAppendBase
-
- setSkipMissingChannels(boolean) - Method in class NamedChannelsAppend
-
- setSkipNumberSubdirectories(int) - Method in class LastDirectories
-
Initially skip this number of directories before including them in the description.
- setSlice(ChannelProvider) - Method in class RepeatSlice
-
- setSliceFirst(int) - Method in class MontageSlices
-
First slice.
- setSliceID(int) - Method in class SelectSlicesBase
-
Index of slice to use, or -1 to use all slices
- setSliceIndex(int) - Method in class RepeatSlice
-
Which slice to use from mask
- setSliceLast(int) - Method in class MontageSlices
-
Last slice.
- setSlicesSeparately(boolean) - Method in class FitBoxToOnVoxels
-
- setSmoothingFactor(double) - Method in class SplitContourAtSaddlePoints
-
- setSource(String) - Method in class StringMapItem
-
The origin of the mapping.
- setSource(FeatureSource<T, S, U>) - Method in class ExportFeatures
-
Source of feature-values to be exported.
- setSources(List<NamedBean<ComparableSource>>) - Method in class MultipleComparer
-
The other entities to compare with the annotation.
- setSplitIdentifierRegex(String) - Method in class CompareAnnotations
-
If non-empty, the string (a regular-expression) is used to split the file's identifier into
groups.
- setSplitProposer(MarkSplitProposer) - Method in class KernelSplit
-
- setSquareSize(int) - Method in class SplitIntoSquares
-
- setStack(Provider<Stack>) - Method in class StackProviderUnary
-
- setStack(Provider<Stack>) - Method in class StackProviderWithLabel
-
- setStack(DisplayStack) - Method in class ColoredMarksWithDisplayStack
-
- setStack(DisplayStack) - Method in class MarksWithDisplayStack
-
- setStack(ProviderAsStack) - Method in class FromStack
-
Provides a stack.
- setStack(ProviderAsStack) - Method in class SegmentStack
-
The stack to segment
- setStack(StackProvider) - Method in class ExportObjectsFromCSV
-
The stack that is the background for our objects
- setStackAsChannel(boolean) - Method in class MultiInputManagerQuick
-
If true, a raster-stack is treated as a single-channel, even if multiple exist (and no
additionalChannel is set)
- setStackBackground(boolean) - Method in class VisualizeOnBackground
-
- setStackEnergy(Provider<Stack>) - Method in class FeatureEvaluator
-
Optionally specifies an energy-stack to be associated with every calculation input.
- setStackEnergy(StackProvider) - Method in class FromImage
-
Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is
considered to be the input stacks).
- setStackEnergy(StackProvider) - Method in class BinaryClassifierImageLabeller
-
- setStackEnergy(StackProvider) - Method in class ExtractSlice
-
- setStackEnergy(StackProvider) - Method in class DefineOutputterWithEnergy
-
- setStackID(String) - Method in class IfStackExists
-
- setStackName(String) - Method in class One
-
If defined, processing only occurs the stack with this specific stack and index.
- setStackNameDefault(String) - Method in class AnnotationBackground
-
The name of the default stack from backgroundStackMap to display as background when
annotating.
- setStackProviderID(String) - Method in class FromStack
-
Specifies the ID of an existing stack.
- setStackProviderID(String) - Method in class FromStackChannel
-
- setStackReader(StackReader) - Method in class AnnotatorStrategy
-
How to read raster
Stacks from the file-system.
- setStackReader(StackReader) - Method in class InputManagerWithStackReader
-
- setStackReader(StackReader) - Method in class MaskAsObject
-
How to read the
Mask from the file-system.
- setStackReader(StackReader) - Method in class FromStackReader
-
- setStackReader(StackReader) - Method in class FlattenAsChannel
-
Reads the image that is subsequently flattened.
- setStackReader(StackReader) - Method in class ImposeResolution
-
Reads an image before a resolution is imposed.
- setStackReader(StackReader) - Method in class MultiFileReader
-
- setStackReader(StackReader) - Method in class ReadVoxelExtentXml
-
Reads an image before a resolution is imposed.
- setStackReader(StackReader) - Method in class RejectIfConditionXYResolution
-
Reads an image before a resolution is imposed.
- setStackReaderAdjacent(StackReader) - Method in class NamedChannelsQuick
-
The raster-reader to use for opening any adjacent-channels
- setStackReaderAppend(StackReader) - Method in class QuickBase
-
The raster-reader for reading any appended files
- setStart(int) - Method in class SequenceInteger
-
The index to begin iteration from.
- setStartIndex(int) - Method in class MovieFromSlices
-
- setStartingIntensity(int) - Method in class FloodFillEachIntensityLevel
-
The first intensity-value to consider as a valid object (e.g.
- setStateReporter(StateReporter<T, S>) - Method in class TransformationAssignMode
-
- setStrategy(BlurStrategy) - Method in class Blur
-
- setStringRasterGenerator(TextStyle) - Method in class GenerateString
-
- setStrongEdgeEnhancer(boolean) - Method in class AnisotropicDiffusion
-
If true uses, the strong-edge-enhancer diffusion function, otherwise the wide-region-enhancer.
- setStyle(ExportFeaturesStyle) - Method in class ExportFeatures
-
Visual style for how feature export occurs.
- setStyle(ExportFeaturesStyle) - Method in class SegmentInstanceWithModel
-
Visual style for how feature export occurs.
- setSubdirectory(String) - Method in class AppendDictionary
-
- setSubdirectory(String) - Method in class ExperimentResultsExperimentStructure
-
If non-empty than an additional subdirectory is appended as a suffix
${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
- setSubtractConstant(int) - Method in class IntensityGradientBase
-
- setSubtractFromMaskOnly(boolean) - Method in class SubtractMean
-
- setSubtractRadii(double) - Method in class ConicFitterBase
-
- setSummarizer(Summarizer<S>) - Method in class SummarizerInputFromManager
-
- setSummarizer(Summarizer<S>) - Method in class SummarizeBase
-
- setSummarizerElse(Summarizer<T>) - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) <= countThreshold
- setSummarizerGreaterThan(Summarizer<T>) - Method in class SummarizerSplitMoreThan
-
Used for summary if count(elements) > countThreshold
- setSuppress3D(boolean) - Method in class MorphologicalOperatorBase
-
- setSuppress3D(boolean) - Method in class SurfaceNumberVoxelsBase
-
- setSuppress3D(boolean) - Method in class SegmentThresholdAboveMinBound
-
- setSuppressDirectories(boolean) - Method in class FromDescriptiveName
-
If true, any directory separators in the identifier in a descriptive-name are replaced by
underscores.
- setSuppressErrors(boolean) - Method in class ExportFeaturesStyle
-
When false, an image is reported as errored, if any exception is thrown during calculation.
- setSuppressErrors(boolean) - Method in class FromObjects
-
When true, exceptions aren't thrown when feature-calculations fail, but rather a log error
message is written.
- setSuppressExceptions(boolean) - Method in class JobProcessor
-
- setSuppressExceptions(boolean) - Method in class QuickMultiDatasetExperiment
-
- setSuppressExceptions(boolean) - Method in class QuickMultiDatasetStructuredExperiment
-
- setSuppressOutlineZ(boolean) - Method in class ColoredBase
-
if true, the outline is suppressed in the z-dimension i.e.
- setSuppressRes(boolean) - Method in class RadiiRatio
-
- setSuppressRootOut(boolean) - Method in class Rooted
-
if true, the root is not added to the outFilePath, and the path is instead localized against
the location of the BeanXML.
- setSuppressSeries(boolean) - Method in class ConvertImageFormat
-
If true, the series index is not included in the outputted file-names.
- setSuppressSubfolders(boolean) - Method in class DefineOutputter
-
- setSuppressZ(boolean) - Method in class BoundingBoxIntersection
-
- setSuppressZ(boolean) - Method in class DistanceTransform3D
-
- setSuppressZ(boolean) - Method in class DistanceTransformForEachObject3D
-
- setSuppressZ(boolean) - Method in class MergeWithOptionalDistanceConstraint
-
- setSuppressZ(boolean) - Method in class CostOverlapWithinMidpointDistance
-
- setSuppressZ(boolean) - Method in class ImageMomentsBase
-
If true co-voariance is suprpessed in z-dimension
- setSuppressZ(boolean) - Method in class CenterOnMask
-
- setSuppressZ(boolean) - Method in class UniformRandom
-
- setSuppressZ(boolean) - Method in class SurfaceSizeMaskNonZero
-
- setSuppressZ(boolean) - Method in class EllipsoidBase
-
Iff true, surpresses covariance in the z-direction.
- setSuppressZCovariance(boolean) - Method in class FromObjects
-
- setSuppressZCovariance(boolean) - Method in class LinearLeastSquaresEllipsoidFitter
-
- setTarget(String) - Method in class StringMapItem
-
The destination of the mapping.
- setTargetSize(SizeXY) - Method in class FitTo
-
The target size.
- setTask(Task<T, S>) - Method in class JobProcessor
-
- setTask(SelectParam<Optional<Path>>) - Method in class ExperimentExecutor
-
- setTask(Task<U, S>) - Method in class ConvertNamedChannels
-
The underlying task that will be called, perhaps with a different input-type.
- setTask(Task<MultiInput, S>) - Method in class QuickExperiment
-
- setTask(Task<T, S>) - Method in class QuickMultiDatasetExperiment
-
- setTask(Task<T, S>) - Method in class QuickMultiDatasetStructuredExperiment
-
- setTaskProcessor(JobProcessor<T, S>) - Method in class InputOutputExperiment
-
What task is associated with the experiment, and how it is processed.
- setTemperature(double) - Method in class OptimizationStep
-
- setTemplateMark(MarkFactory) - Method in class MarkWithIdentifierFactory
-
- setTermination(TerminationCondition) - Method in class SimulatedAnnealing
-
- setText(String) - Method in class GenerateString
-
Text to draw on an image
- setThreshold(double) - Method in class RelationToConstant
-
The constant threshold.
- setThreshold(int) - Method in class CutBelowThreshold
-
- setThreshold(int) - Method in class CalculateLevelRelativeToThreshold
-
- setThreshold(UnitValueDistance) - Method in class IntensityGreaterEqualThan
-
- setThreshold(double) - Method in class ThresholdedFeature
-
- setThreshold(UnitValueVolume) - Method in class ThresholdedVolume
-
- setThreshold(RelationToThreshold) - Method in class Count
-
- setThreshold(RelationToThreshold) - Method in class RatioThreshold
-
- setThreshold(double) - Method in class FeatureIntersectingObjectsThreshold
-
Only considers values greater or equal to the threshold
- setThreshold(double) - Method in class AddCriteriaFeatureRelationThreshold
-
- setThreshold(double) - Method in class RequireFeatureRelationThreshold
-
- setThreshold(RelationToThreshold) - Method in class GreatestAreaSlice
-
- setThreshold(RelationToThreshold) - Method in class Thresholded
-
- setThreshold(RelationToThreshold) - Method in class IfCondition
-
- setThresholder(Thresholder) - Method in class BinarySegmentationThreshold
-
- setThresholder(Thresholder) - Method in class Threshold
-
The thresholder that will convert a channel into a binary-channel
- setThresholdHours(double) - Method in class ClusterByTimestamp
-
Files whose creation-time differs <= this parameter are joined into the same cluster.
- setThresholdNumberObjectsGlobal(int) - Method in class ThresholdConfidence
-
When the number of objects is greater or equal than this, they are reduced globally, without
separation.
- setThrowExceptionForInsufficientPoints(boolean) - Method in class CreateMarkFromPoints
-
- setThumbnail(ThumbnailFromObjects) - Method in class CombineObjectsForFeatures
-
Generates a thumbnail representation of one or more combined objects, as form a single input.
- setThumbnail(ThumbnailFromStack) - Method in class FromImage
-
Method to generate a thumbnail for images.
- setTime(boolean) - Method in class ExperimentIdentifierAuto
-
If true, the current time (HH.mm.ss) is included in the output
- setTimeIndex(int) - Method in class ConvertNamedChannelsToStack
-
- setTimeIndexGroupID(int) - Method in class RegularExpression
-
- setTimes(int) - Method in class Repeat
-
How many times to duplicate the list.
- setTimestampPatterns(List<TimestampPattern>) - Method in class ClusterByTimestamp
-
The patterns which can be used to extract a date-time from a filename.
- setTimeZoneOffset(int) - Method in class ClusterByTimestamp
-
If >= 0, sets a specific time-offset in hours.
- setTitle(String) - Method in class ReportFeatureEvaluator
-
- setTitle(String) - Method in class ReportFeatureForManifestFileBase
-
- setTolerance(int) - Method in class UnchangedScore
-
An exponent of 10 which determines a tolerance, less than which a score will be deemed
unchanged compared to another.
- setTransformer(StateTransformerBean<MarkCollection, T>) - Method in class RemovePartitionAndThen
-
- setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class VoxelizeWithTransform
-
- setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class KernelStateBridgePixelize
-
- setTransformerKernelToState(StateTransformerBean<U, T>) - Method in class KernelStateBridgeTransformer
-
- setTransformerMarks(StateTransformerBean<MarkCollection, VoxelizedMarksWithEnergy>) - Method in class AddDualTransformer
-
- setTransformerPrimary(StateTransformerBean<T, S>) - Method in class StateReporterTransformer
-
- setTransformerSecondary(StateTransformerBean<T, S>) - Method in class StateReporterTransformer
-
- setTransformerStateToKernel(StateTransformerBean<T, U>) - Method in class KernelStateBridgeTransformer
-
- setTransposed(boolean) - Method in class CombineCSV
-
- setTrimTrailingDirectory(int) - Method in class RemoveTrailingDirectory
-
- setTrimTrailingDirectory(int) - Method in class FilePathAppendBase
-
- setUniqueLabel(String) - Method in class AnnotationLabel
-
Label that uniquely identifies the ID (for machine purposes)
- setUnit(UnitConverter) - Method in class BoundingBoxExtent
-
- setUnit(UnitConverter) - Method in class FeatureSingleMemoRegion
-
- setUnitType(String) - Method in class DistancePhysical
-
- setUnitType(String) - Method in class AreaPhysical
-
- setUnitType(String) - Method in class VolumePhysical
-
- setUnitType(String) - Method in class FeatureConvertUnits
-
- setUnitType(String) - Method in class UnitConverter
-
- setUnitTypeFrom(String) - Method in class ConvertUnits
-
- setUnitTypeTo(String) - Method in class ConvertUnits
-
- setUnitValueDistance(UnitValueDistance) - Method in class FromUnitValueDistance
-
- setupBefore(Dimensions, ImageFileEncoding) - Method in class ConvertTo
-
- setupBefore(Dimensions, ImageFileEncoding) - Method in class FloatFromUnsignedByte
-
- setupDictionary(Dictionary) - Method in class FromDictionaryBase
-
- setUseLastSeriesIndexOnly(boolean) - Method in class NamedChannels
-
- setUseLastSeriesIndexOnly(boolean) - Method in class Stacks
-
- setUseMax(boolean) - Method in class OverlapRatio
-
- setUseMax(boolean) - Method in class OverlapRatioMask
-
- setUserFriendlyLabel(String) - Method in class AnnotationLabel
-
Descriptive user-friendly label displayed via GUI
- setUseZ(boolean) - Method in class RemoveTouchingBorder
-
- setUseZ(boolean) - Method in class TraverseOuterContourOnImage
-
- setValue(T) - Method in class NamedBean
-
- setValue(T) - Method in interface NameValue
-
Assigns the associated value.
- setValue(V) - Method in class SimpleNameValue
-
- setValue(double) - Method in class Constant
-
The constant value.
- setValue(double) - Method in class DistancePhysical
-
- setValue(double) - Method in class DistanceVoxels
-
- setValue(double) - Method in class UnitValueArea
-
- setValue(double) - Method in class VolumePhysical
-
- setValue(double) - Method in class VolumeVoxels
-
- setValue(double) - Method in class AssignValue
-
- setValue(int) - Method in class CreateNew
-
- setValue(double) - Method in class UnaryWithValueBase
-
- setValue(String) - Method in class DictionaryCondition
-
The value the key should have in the dictionary, in order for the condition to be fulfilled.
- setValue(int) - Method in class EmptyHistogramConstant
-
- setValue(String) - Method in class IfParamEqual
-
- setValue(double) - Method in class ConstantScaleFactor
-
- setValue(int) - Method in class CountEqual
-
- setValue(double) - Method in class IdentityImposeValueRelationToHistogram
-
- setValue(double) - Method in class NormalizeByConstant
-
- setValue(String) - Method in class Constant
-
- setValue(double) - Method in class Constant
-
- setValue(double) - Method in class WithValueBase
-
- setValueByDimension(int, double) - Method in class Tuple3d
-
Assigns a value to a component of the tuple corresponding to a particular dimension by index.
- setValueByDimension(int, float) - Method in class Tuple3f
-
Assigns a value to a component of a tuple corresponding to a particular dimension by index.
- setValueIfEmpty(double) - Method in class FeatureHistogramStatistic
-
The value to return iff exceptionifEmpty is false.
- setValueIfTooFewVoxels(double) - Method in class ImageMomentsBase
-
A value to return if there are too few voxels (less than MIN_NUM_VOXELS to calculate
moments
- setValueNoObject(int) - Method in class ScoreObjects
-
- setValueNoObjects(double) - Method in class FeatureIntersectingObjects
-
- setValues(DoubleSet) - Method in class PermutePropertyDoubleSet
-
The respect double values to assign during the permutation.
- setValues(StringSet) - Method in class PermutePropertyStringSet
-
The respect string values to assign during the permutation.
- setVaryColors(boolean) - Method in class SegmentInstanceWithModel
-
If true the colors change for different objects in the image (using a default color set).
- setVersion(String) - Method in class ExperimentIdentifierConstant
-
- setVerticalAlign(String) - Method in class Overlay
-
- setVisitScheduler(VisitScheduler) - Method in class TraverseOuterContourOnImage
-
- setVisuallyShortenDecimals(boolean) - Method in class ExportFeaturesStyle
-
When true, feature-values are shown as visually compressed as possible, including suppressing
decimal places.
- setWeight(double) - Method in class KernelProposerOptionSingle
-
- setWeightBackground(double) - Method in class OtsuWeighted
-
- setWeightForeground(double) - Method in class OtsuWeighted
-
- setWeightItem1Greater(double) - Method in class Range
-
- setWeightItem2Greater(double) - Method in class Range
-
- setWeightNegative(double) - Method in class KernelProposerOptionDual
-
- setWeightPositive(double) - Method in class KernelProposerOptionDual
-
- setWeightWidthDescription(int) - Method in class ImageLabelStrategy
-
- setWhenBinaryChannel(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled binary image.
- setWhenDetailed(LoggingDestination) - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is on
- setWhenEqual(ObjectCollectionProvider) - Method in class IfParamEqual
-
- setWhenFalse(DrawObject) - Method in class IfElse
-
- setWhenNot(LoggingDestination) - Method in class SwitchDetailedLogging
-
Logger to use when detailed-logging is off
- setWhenNotEightBit(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack contains channels that are not 8-bit.
- setWhenNotEqual(ObjectCollectionProvider) - Method in class IfParamEqual
-
- setWhenRelative(FileNamer) - Method in class IfRelativeToDirectory
-
The namer to use if the relative-to-directory option is selected.
- setWhenRGB(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled RGB image.
- setWhenRGBAlpha(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a four-channeled RGBA image.
- setWhenSingleChannel(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a single-channeled image, not guaranteed to be binary.
- setWhenThreeChannels(StackWriter) - Method in class BranchChannels
-
Writer employed if a stack is a three-channeled non-RGB image.
- setWhenTrue(DrawObject) - Method in class IfElse
-
- setWidth(int) - Method in class SizeXY
-
Size in X dimension.
- setWidth(double) - Method in class Difference
-
Width (what the difference is divided by)
- setWidth(double) - Method in class ImposeResolution
-
Physical pixel size of a voxel in x-dimension.
- setWidthFactor(double) - Method in class DifferenceCalculateLevelStandardDeviation
-
- setWindowSize(int) - Method in class CenterSliceWindow
-
- setWindowSize(SizeXY) - Method in class HOGParameters
-
The window-size as per OpenCV implementation.
- setWithin(double) - Method in class UnitsWithinRange
-
Returned as a constant if a value lies within the range
- setWithinValue(double) - Method in class CompareWithRange
-
Constant to return if value lies within the range
- setWithinValue(double) - Method in class CompareWithRangeFeature
-
Constant to return if value lies within the range
- setWriter(DrawObject) - Method in class Flatten
-
- setWriter(StackWriter) - Method in class BranchChannels
-
Default writer, if a more specific writer is not specified for a condition.
- setWriter(StackWriter) - Method in class WriteResolutionXml
-
- setWriterAlways2D(StackWriter) - Method in class BranchStack
-
Writer to use if it is guaranteed that the image will always be 2D.
- setWriterElse(StackWriter) - Method in class BranchStack
-
Otherwise the writer to use.
- setWriterIfNoSuggestion(StackWriter) - Method in class BranchSuggestedFormat
-
The writer to use if there is no suggested file-format.
- setWriters(List<NamedBean<?>>) - Method in class OutputWriteSettings
-
Specifies a writer bean instance for a particular type of writer (identified by the writer
bean class)
- setWritersIfSuggested(List<StackWriter>) - Method in class BranchSuggestedFormat
-
A list of writers to select if a given format is used
- setX(double) - Method in class VectorInDirection
-
- setX(String) - Method in class PlotAxisLabels
-
- setX(int) - Method in class Point2i
-
X-axis component of point.
- setX(int) - Method in class Tuple3d
-
X-axis component of the tuple.
- setX(double) - Method in class Tuple3d
-
X-axis component of the tuple.
- setX(int) - Method in class Tuple3i
-
X-axis component of the tuple.
- setXDiv(double) - Method in class Orientation
-
- setXY(String, String) - Method in class PlotAxisLabels
-
- setY(double) - Method in class VectorInDirection
-
- setY(String) - Method in class PlotAxisLabels
-
- setY(int) - Method in class Point2i
-
Y-axis component of point.
- setY(int) - Method in class Tuple3d
-
Y-axis component of the tuple.
- setY(double) - Method in class Tuple3d
-
Y-axis component of the tuple.
- setY(int) - Method in class Tuple3i
-
Y-axis component of the tuple.
- setYAxisLowerMargin(double) - Method in class LinePlot
-
- setYAxisMargins(double) - Method in class LinePlot
-
- setYAxisUpperMargin(double) - Method in class LinePlot
-
- setYValGetter(LinePlot.YValGetter<T>) - Method in class LinePlot
-
- setZ(double) - Method in class VectorInDirection
-
- setZ(int) - Method in class Tuple3d
-
Z-axis component of the tuple.
- setZ(double) - Method in class Tuple3d
-
Z-axis component of the tuple.
- setZ(int) - Method in class Tuple3i
-
Z-axis component of the tuple.
- setZAlign(String) - Method in class Overlay
-
- setZSliceGroupID(int) - Method in class RegularExpression
-
- setZSliceNum(int) - Method in class SortedSetSlice
-
- shallowCopy() - Method in class ColorList
-
Creates a new list, containing the same elements as the current list.
- shallowCopy() - Method in class GraphWithPayload
-
Creates a new graph with identical elements and structure, reusing the existing vertice and
edge data objects.
- shallowCopy() - Method in class RandomCollectionWithAddCriteria
-
- shallowCopy() - Method in class MarksWithEnergyBreakdown
-
- shallowCopy() - Method in class MarksWithTotalEnergy
-
Make a shallow copy
- shallowCopy() - Method in class VoxelizedMarksWithEnergy
-
Creates a shallow-copy of the marks
- shallowCopy() - Method in class EnergySavedAll
-
- shallowCopy() - Method in class EnergySavedInd
-
- shallowCopy() - Method in class EnergySavedPairs
-
- shallowCopy() - Method in class ColoredMarks
-
- shallowCopy() - Method in class MarkCollection
-
- shallowCopy() - Method in class OverlayCollection
-
- shallowDuplicate() - Method in class FeatureList
-
Creates a new feature-list which contains identical elements.
- ShapeRegularityCenterSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- ShapeRegularityCenterSlice() - Constructor for class ShapeRegularityCenterSlice
-
- ShapeRegularityMIP - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
-
- ShapeRegularityMIP() - Constructor for class ShapeRegularityMIP
-
- SharedFeatures - Class in org.anchoranalysis.feature.shared
-
A group of features made available to other features to reference.
- SharedFeatures() - Constructor for class SharedFeatures
-
Create empty, without any features.
- SharedFeaturesSubset<T extends FeatureInput> - Class in org.anchoranalysis.feature.shared
-
A subset of features from
SharedFeatures that share a common feature input-type.
- SharedFeaturesSubset(NameValueMap<Feature<T>>) - Constructor for class SharedFeaturesSubset
-
- SharedObjects - Class in org.anchoranalysis.core.identifier.provider.store
-
Objects shared between different components.
- SharedObjects(CommonContext) - Constructor for class SharedObjects
-
- sharedObjectsRequired() - Method in class FeatureInitialization
-
Retrieves the shared-objects associated with the initialization, or throws an an exception if
they do not exist.
- SharedStateFilteredImageOutput<T> - Class in org.anchoranalysis.plugin.image.task.labeller
-
- SharedStateFilteredImageOutput(Outputter, ImageLabeller<T>, String, String) - Constructor for class SharedStateFilteredImageOutput
-
- SharedStateRememberConverted<U extends InputFromManager,S> - Class in org.anchoranalysis.plugin.mpp.experiment.shared
-
Shared-state that remembers converted inputs for corresponding unconverted inputs.
- SharedStateRememberConverted() - Constructor for class SharedStateRememberConverted
-
- SharedStateSegmentInstance<T extends InferenceModel> - Class in org.anchoranalysis.plugin.image.task.segment
-
Shared-state for instance segmentation
- SharedStateSegmentInstance(ConcurrentModelPool<T>, FeatureTableCalculator<FeatureInputSingleObject>, LabelHeaders, String, FeatureExporterContext) - Constructor for class SharedStateSegmentInstance
-
- SharedStateSelectedSlice - Class in org.anchoranalysis.plugin.image.task.stack
-
- SharedStateSelectedSlice(Outputter) - Constructor for class SharedStateSelectedSlice
-
- Shell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
-
- Shell() - Constructor for class Shell
-
- shift() - Method in class SlidingBuffer
-
Increments the slice number by one.
- shiftBackBy(VoxelsAssigner, ReadableTuple3i) - Static method in class VoxelsAssignerFactory
-
Shifts all coordinates
backwards before passing to another
VoxelsAssigner.
- shiftBackBy(ReadableTuple3i) - Method in class ObjectMask
-
Shifts the object-mask by moving its bounding-box backwards.
- shiftBackBy(ReadableTuple3i) - Method in class BoundingBox
-
Shifts the bounding-box backwards.
- shiftBy(T, ReadableTuple3i) - Method in interface AccessObjectMask
-
Positionally-shifts an element by a given quantity in the positive direction.
- shiftBy(ObjectMask, ReadableTuple3i) - Method in class AccessObjectMaskSimple
-
- shiftBy(ReadableTuple3i) - Method in class ObjectCollection
-
Shifts the bounding-box of each object by adding to it.
- shiftBy(ReadableTuple3i) - Method in class ObjectMask
-
Shifts the object-mask by moving its bounding-box forwards.
- shiftBy(ReadableTuple3i) - Method in class BoundingBox
-
Shifts the bounding-box forwards.
- shiftTo(Point3i) - Method in class BoundingBox
-
Assigns a new corner-location to the bounding-box.
- shiftToOrigin() - Method in class ObjectMask
-
Creates a new object-mask with identical voxels but with the bounding-box beginning at the
origin (0,0,0).
- shiftToOrigin() - Method in class BoundingBox
-
Moves the bounding-box to the origin (0,0,0) but preserves the extent.
- shiftToZ(int) - Method in class BoundingBox
-
Assigns a new z-slice corner-location to the bounding-box.
- SHORT_OPTION_DEBUG - Static variable in class CommandLineOptions
-
Enables debug-mode: runs only the first available input [whose name contains string].
- SHORT_OPTION_HELP - Static variable in class CommandLineOptions
-
Displays help message with all command-line options.
- SHORT_OPTION_INPUT - Static variable in class CommandLineOptions
-
Changes inputs.
- SHORT_OPTION_INPUT_COPY_NON_INPUTS - Static variable in class CommandLineOptions
-
Additionally copies any files in the input directory, unused as inputs.
- SHORT_OPTION_INPUT_RELATIVE - Static variable in class CommandLineOptions
-
Derives the unique identifier from the **entire relative filename or path** (excluding file
extension).
- SHORT_OPTION_INPUT_SHUFFLE - Static variable in class CommandLineOptions
-
Shuffles the order of the inputs.
- SHORT_OPTION_INPUT_SUBSET_IDENTIFIER - Static variable in class CommandLineOptions
-
Subsets the identifier.
- SHORT_OPTION_LOG_ERROR - Static variable in class CommandLineOptions
-
Logs initial BeanXML errors in greater detail to a file-path.
- SHORT_OPTION_OUTPUT - Static variable in class CommandLineOptions
-
Changes output manager.
- SHORT_OPTION_OUTPUT_CONSOLE_ONLY - Static variable in class CommandLineOptions
-
Output console only.
- SHORT_OPTION_OUTPUT_DISABLE_ADDITIONAL - Static variable in class CommandLineOptions
-
Disables specific output(s).
- SHORT_OPTION_OUTPUT_ENABLE_ADDITIONAL - Static variable in class CommandLineOptions
-
Enables all outputs.
- SHORT_OPTION_OUTPUT_ENABLE_ALL - Static variable in class CommandLineOptions
-
Enables specific output(s).
- SHORT_OPTION_OUTPUT_IMAGE_FILE_FORMAT - Static variable in class CommandLineOptions
-
Suggests an output image file format: e.g -of jpg or -of ome.xml.
- SHORT_OPTION_OUTPUT_INCREMENTING_NUMBER - Static variable in class CommandLineOptions
-
Outputs with an incrementing number instead of the input identifier.
- SHORT_OPTION_OUTPUT_OMIT_EXPERIMENT_IDENTIFIER - Static variable in class CommandLineOptions
-
Ignores the experiment identifier, when forming an output-path.
- SHORT_OPTION_OUTPUT_SUPPRESS_DIRECTORIES - Static variable in class CommandLineOptions
-
Suppressed the subdirectory structure when outputting file identifiers.
- SHORT_OPTION_SHOW_EXPERIMENT_ARGUMENTS - Static variable in class CommandLineOptions
-
Shows additional argument information, otherwise executes as normal.
- SHORT_OPTION_SHOW_TASKS - Static variable in class CommandLineOptions
-
Prints the names of predefined tasks that can be easily used with -t.
- SHORT_OPTION_TASK - Static variable in class CommandLineOptions
-
Changes task.
- SHORT_OPTION_TASK_NUMBER_PROCESSORS - Static variable in class CommandLineOptions
-
Suggests a maximum number of processors to use for the task.
- SHORT_OPTION_TASK_SIZE - Static variable in class CommandLineOptions
-
Suggests dimensions or a scaling factor for certain tasks.
- SHORT_OPTION_VERSION - Static variable in class CommandLineOptions
-
Displays version and authorship information.
- shouldOverwriteVoxelWithConstant(int, int) - Method in class ArithmeticWithConstantConditionallyWriteBase
-
Whether to overwrite the current voxel-value with the constant?
- shouldOverwriteVoxelWithConstant(int, int) - Method in class MaxWithConstant
-
- shouldOverwriteVoxelWithConstant(int, int) - Method in class MinWithConstant
-
- shouldVisitPoint(Point3i, int) - Method in interface ConsiderVisit
-
Determines whether to visit a point or not.
- Shuffle - Class in org.anchoranalysis.bean.shared.color.scheme
-
Randomizes the order of colors in a list created by another
ColorScheme.
- Shuffle(ColorScheme) - Constructor for class Shuffle
-
- Shuffle() - Constructor for class Shuffle
-
- shuffle() - Method in class ColorList
-
Randomize the order of the colors in the list.
- Shuffle<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Randomly shuffles the order of the inputs.
- Shuffle() - Constructor for class Shuffle
-
- ShuffleIfRequested<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
- ShuffleIfRequested() - Constructor for class ShuffleIfRequested
-
- SignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype
-
A 16-bit voxel data-type representing signed-short numbers.
- SignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype
-
Base class for voxel-data-types that are signed and integral.
- SignedVoxelType(int, String, long, long) - Constructor for class SignedVoxelType
-
Construct for a particular number of bits, with a unique identifier, and with bounds on the
values.
- SimpleAnnotationDeleter - Class in org.anchoranalysis.annotation.io
-
Deletes any annotation when it is represented by a single file.
- SimpleAnnotationDeleter() - Constructor for class SimpleAnnotationDeleter
-
- SimpleManifestDeserializer - Class in org.anchoranalysis.io.manifest.deserializer
-
- SimpleManifestDeserializer() - Constructor for class SimpleManifestDeserializer
-
- SimpleName - Class in org.anchoranalysis.feature.io.name
-
A name with only one part, and is always unique.
- SimpleName(String) - Constructor for class SimpleName
-
- SimpleNameValue<V> - Class in org.anchoranalysis.core.identifier.name
-
A simple container expressing a name-value pair.
- SimpleNameValue(String, V) - Constructor for class SimpleNameValue
-
- SimpleOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
- SimpleOutputNameStyle(String) - Constructor for class SimpleOutputNameStyle
-
- SimpleOverlayWriter - Class in org.anchoranalysis.mpp.io.marks.generator
-
Converts a configuration to a set of object-masks, using a simple
DrawObject for all
objects.
- SimpleOverlayWriter(DrawObject) - Constructor for class SimpleOverlayWriter
-
- SimulatedAnnealing<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
-
Finds an optima using a simulated-annealing approach
- SimulatedAnnealing() - Constructor for class SimulatedAnnealing
-
- Single - Class in org.anchoranalysis.image.bean.spatial.arrange
-
- Single() - Constructor for class Single
-
- Single - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
-
- Single() - Constructor for class Single
-
- SingleChannel - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
A score that is calculated on a single channel only
- SingleChannel() - Constructor for class SingleChannel
-
- SingleChannel - Class in org.anchoranalysis.plugin.io.bean.channel.map
-
For an image with a single channel
- SingleChannel() - Constructor for class SingleChannel
-
- SingleChannel(String) - Constructor for class SingleChannel
-
- singleChannelMaybe3D(boolean) - Static method in class StackWriteAttributesFactory
-
- SingleColor - Class in org.anchoranalysis.core.color
-
An index that always uses the same single color
- SingleColor(Color) - Constructor for class SingleColor
-
Creates with a particular color.
- SingleColor(RGBColor) - Constructor for class SingleColor
-
- SingleFile - Class in org.anchoranalysis.io.input.bean.files
-
- SingleFile(String) - Constructor for class SingleFile
-
- SingleFile() - Constructor for class SingleFile
-
- SingleFileInputBase - Class in org.anchoranalysis.io.input.file
-
A base class for inputs that refer to a single file.
- SingleFileInputBase(NamedFile) - Constructor for class SingleFileInputBase
-
- SingleFileTypeGenerator<T,S> - Class in org.anchoranalysis.io.generator
-
A
Generator that eventually writes only a single file to the filesystem.
- SingleFileTypeGenerator() - Constructor for class SingleFileTypeGenerator
-
- SingleFileTypeGeneratorBridge<S,T,V> - Class in org.anchoranalysis.io.generator
-
Allows us to call an SingleFileTypeGenerator<V,S> as if it was an SingleFileTypeGenerator<T,S> using an function to connect the two.
- SingleFileTypeGeneratorBridge(SingleFileTypeGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class SingleFileTypeGeneratorBridge
-
- SingleLevelAnd - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelAnd(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelAnd
-
- SingleLevelBinary - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelBinary(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelBinary
-
- SingleLevelInSet - Class in org.anchoranalysis.io.output.enabled.single
-
Outputs are enabled if they are contained in a set.
- SingleLevelInSet(Set<String>) - Constructor for class SingleLevelInSet
-
- SingleLevelNot - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelNot(SingleLevelOutputEnabled) - Constructor for class SingleLevelNot
-
- SingleLevelOr - Class in org.anchoranalysis.io.output.enabled.single
-
- SingleLevelOr(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class SingleLevelOr
-
- SingleLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.single
-
- SingleMarkProvider - Class in org.anchoranalysis.mpp.bean.provider
-
Provides (maybe) a single mark
- SingleMarkProvider() - Constructor for class SingleMarkProvider
-
- SinglePathStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
-
A base class for implementations of
AnnotatorStrategy where a single unique path exists
for every annotation.
- SinglePathStrategy() - Constructor for class SinglePathStrategy
-
- SingleRowPerInput<T extends InputFromManager,S extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source
-
Base class for exporting features, where features are calculated per-image using a
NamedFeatureStore.
- SingleRowPerInput(String) - Constructor for class SingleRowPerInput
-
Creates with a single non-group header that should be describe an identifier.
- SingleRowPerInput(String[]) - Constructor for class SingleRowPerInput
-
- SingleTableCalculator - Class in org.anchoranalysis.image.feature.calculator
-
- SingleTableCalculator(NamedFeatureStore<FeatureInputSingleObject>) - Constructor for class SingleTableCalculator
-
- size() - Method in class ColorList
-
The number of elements (colors) in the list.
- size() - Method in class NameValueMap
-
The number of elements in the set.
- size() - Method in class FeatureList
-
Returns the number of elements in this list.
- size() - Method in class LabelledResultsVector
-
The number of calculations stored in the vector.
- size() - Method in class FeatureNameList
-
The number of names in the list.
- size() - Method in class ResultsVector
-
The number of calculations stored in the vector.
- size() - Method in class ResultsVectorList
-
- size() - Method in class NamedFeatureStore
-
The total number of
Features in the store.
- size() - Method in class ObjectCollectionWithProperties
-
Number of elements in the collection.
- size() - Method in class ScaledElements
-
Number of scaled-elements.
- size() - Method in class NamedStacks
-
Number of stacks.
- size() - Method in class StackSeries
-
- size() - Method in class TimeSequence
-
- size() - Method in class IntersectingObjects
-
Number of items in the r-tree.
- size() - Method in class ObjectCollection
-
The number of objects in the collection.
- size() - Method in interface VoxelStatistics
-
The total count.
- size() - Method in class VoxelStatisticsCombined
-
- size() - Method in class VoxelStatisticsFromHistogram
-
- size() - Method in class Histogram
-
The size of the range of values in the histogram.
- size() - Method in class BoundUnitless
-
- size() - Method in class MarksWithEnergyBreakdown
-
- size() - Method in class MarksWithTotalEnergy
-
- size() - Method in class VoxelizedMarksWithEnergy
-
- size() - Method in class EnergySavedInd
-
- size() - Method in class EnergyMemoList
-
- size() - Method in class MemoList
-
- size() - Method in class UpdatableMarksList
-
- size() - Method in class IndexByChannel
-
- size() - Method in class ColoredMarks
-
- size() - Method in class MarkCollection
-
- size() - Method in interface MemoForIndex
-
- size() - Method in class TerminationConditionListOr
-
- size() - Method in class WeightedKernelList
-
- size() - Method in class ColoredOverlayCollection
-
- size() - Method in class OverlayCollection
-
- size() - Method in class ListWithThumbnails
-
- size() - Method in class ParsedFilePathBag
-
- size() - Method in class ContiguousVoxelPath
-
- size() - Method in class LoopablePoints
-
- Size - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- Size() - Constructor for class Size
-
- size() - Method in class BoundedList
-
The number of elements.
- size() - Method in class RTree
-
The total number of items stored in the tree.
- sizeC(IFormatReader) - Method in class Default
-
- sizeC(IFormatReader) - Method in class ForceNumberChannels
-
- sizeC(IFormatReader) - Method in class ReadOptions
-
Number of channels.
- sizeC(IFormatReader) - Method in class ReadOptionsDelegate
-
- sizeCurrentLoad() - Method in class LRUCache
-
Number of items currently in the cache.
- sizeDescriptor(Extent) - Method in class HOGParameters
-
Calculates the size of the descriptor will be for a given image.
- SizeExtents - Class in org.anchoranalysis.plugin.io.multifile
-
Remembers the different sizes among the files
- SizeExtents(ParsedFilePathBag) - Constructor for class SizeExtents
-
- sizeFeatures() - Method in interface FeatureCalculatorMulti
-
- sizeFeatures() - Method in class FeatureCalculatorMultiChangeInput
-
- sizeFeatures() - Method in class SequentialSession
-
- sizeFeatures() - Method in class PairsTableCalculator
-
- sizeFeatures() - Method in class SingleTableCalculator
-
- sizeFirst() - Method in class CostMatrix
-
The number of elements in the first list.
- sizeSecond() - Method in class CostMatrix
-
The number of elements in the second list.
- sizeT(Progress, Logger) - Method in interface NamedChannelsForSeries
-
- sizeT(Progress, Logger) - Method in class NamedChannelsForSeriesConcatenate
-
- sizeT(Progress, Logger) - Method in class NamedChannelsForSeriesMap
-
- sizeT(IFormatReader) - Method in class Default
-
- sizeT(IFormatReader) - Method in class ForceNumberFrames
-
- sizeT(IFormatReader) - Method in class ForceTimeSeriesToStack
-
- sizeT(IFormatReader) - Method in class ReadOptions
-
Number of time-points (frames in a time series).
- sizeT(IFormatReader) - Method in class ReadOptionsDelegate
-
- SizeXY - Class in org.anchoranalysis.image.bean.spatial
-
- SizeXY(Extent) - Constructor for class SizeXY
-
Constructor
- SizeXY() - Constructor for class SizeXY
-
- SizeXY(int, int) - Constructor for class SizeXY
-
- sizeZ(IFormatReader) - Method in class Default
-
- sizeZ(IFormatReader) - Method in class ForceTimeSeriesToStack
-
- sizeZ(IFormatReader) - Method in class ReadOptions
-
Number of z-slices (slices in a 3D image).
- sizeZ(IFormatReader) - Method in class ReadOptionsDelegate
-
- skewness(Histogram) - Static method in class HistogramStatistics
-
Calculates the skewness of a distribution of values, represented by their histogram.
- Skewness - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
Calculates the
skewness of all the values in
the histogram.
- Skewness() - Constructor for class Skewness
-
- SkipInit - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that this particular bean-field should be ignored during (recursive) initialization.
- slice(int) - Method in class BinaryVoxels
-
- slice(int) - Method in class FromByte
-
- slice(int) - Method in class FromFloat
-
- slice(int) - Method in class FromInt
-
- slice(int) - Method in class FromShort
-
- slice(int) - Method in interface SliceBufferIndex
-
- slice(int) - Method in interface VoxelsExtracter
-
Creates a new
Voxels with only particular slice.
- slice(int) - Method in class Voxels
-
- slice(int) - Method in class VoxelsUntyped
-
- SliceAt - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
-
- SliceAt() - Constructor for class SliceAt
-
- sliceBinary(int) - Method in class BinaryVoxels
-
- sliceBuffer(int) - Method in class Mask
-
A buffer corresponding to a particular z-slice.
- sliceBuffer(int, int) - Method in class RGBStack
-
A buffer corresponding to a particular z-slice of a particular channel.
- sliceBuffer(int) - Method in class BinaryVoxels
-
A buffer corresponding to a particular z-slice.
- sliceBuffer(int) - Method in interface SliceBufferIndex
-
The underlying buffer corresponding to a particular z-slice.
- sliceBuffer(int) - Method in class Voxels
-
A buffer corresponding to a particular z-slice.
- sliceBufferGlobal(int) - Method in class BoundedVoxels
-
A slice buffer with global coordinates.
- sliceBufferGlobal(int) - Method in class ObjectMask
-
A slice buffer with global coordinates.
- SliceBufferIndex<T> - Interface in org.anchoranalysis.image.voxel.buffer.slice
-
A container with voxel-buffers for each z-slice.
- sliceBufferLocal(int) - Method in class ObjectWithProperties
-
A slice buffer with local coordinates.
- sliceBufferLocal(int) - Method in class BoundedVoxels
-
A slice buffer with local coordinates.
- sliceBufferLocal(int) - Method in class ObjectMask
-
A slice buffer with local coordinates.
- slices() - Method in class BinaryVoxels
-
An index mapping slice of voxels (in the z dimension) to a particular buffer with the
corresponding voxel intensities.
- slices() - Method in class Voxels
-
An index mapping slice of voxels (in the z dimension) to a particular buffer with the
corresponding voxel intensities.
- sliceStatisticsForRegion(VoxelizedMark, int) - Method in class IndexedRegionBase
-
- SliceThresholder - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
-
Segmenting a z-
Stack slice-by-slice.
- SliceThresholder(BinaryValuesByte) - Constructor for class SliceThresholder
-
- SliceThresholderMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
-
- SliceThresholderMask(boolean, ObjectMask, BinaryValuesByte) - Constructor for class SliceThresholderMask
-
- SliceThresholderWithoutMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
-
- SliceThresholderWithoutMask(BinaryValuesByte) - Constructor for class SliceThresholderWithoutMask
-
- SlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer
-
An index that places a particular z-slice in local context.
- SlidingBuffer(Voxels<T>) - Constructor for class SlidingBuffer
-
Create for particular voxels.
- Sobel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
3x3 Sobel Filter
- Sobel() - Constructor for class Sobel
-
- solveQuadraticEquation(double, double, double) - Static method in class QuadraticEquationSolver
-
Solves a quadratic equation in form x^2 + b^x + c = 0.
- sort(Comparator<Feature<T>>) - Method in class FeatureList
-
Creates a new feature-list sorted in a particular order.
- SortAlphabetically - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- SortAlphabetically() - Constructor for class SortAlphabetically
-
- SortAlphabetically<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Sorts the input-items in alphabetical order of their input-name.
- SortAlphabetically() - Constructor for class SortAlphabetically
-
- SortAlphabeticallyWithDirectory - Class in org.anchoranalysis.plugin.io.bean.file.provider
-
- SortAlphabeticallyWithDirectory() - Constructor for class SortAlphabeticallyWithDirectory
-
- SortByFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Creates a new object-collection with objects sorted by a derived feature-value (in ascending
order)
- SortByFeature() - Constructor for class SortByFeature
-
- SortedSetChannel - Class in org.anchoranalysis.plugin.io.multifile
-
- SortedSetChannel() - Constructor for class SortedSetChannel
-
- SortedSetSlice - Class in org.anchoranalysis.plugin.io.multifile
-
- SortedSetSlice(String, int) - Constructor for class SortedSetSlice
-
- sourceIncrement - Variable in class ConvertTo
-
The number of elements (bytes) to increment by, when iterating through the source buffer.
- sourceSize - Variable in class ConvertTo
-
The total number of elements (always bytes) in the source buffer.
- sourceValue - Variable in class ProcessVoxelNeighborAbsoluteWithSlidingBuffer
-
The intensity value of the source voxel.
- spatiallySeparate() - Method in class IntersectingObjects
-
Splits the collection of objects into spatially separate clusters.
- SpatiallySeparate<T> - Class in org.anchoranalysis.spatial.rtree
-
Splits a collection of elements into spatially separate clusters.
- SpatiallySeparate(Function<T, BoundingBox>) - Constructor for class SpatiallySeparate
-
- SpatialUnits - Class in org.anchoranalysis.image.core.dimensions
-
Units to describe spatial quantities.
- SpatialUnits.UnitSuffix - Enum in org.anchoranalysis.image.core.dimensions
-
Suffix that describes a particular quantity of units (micron, nano, square microns etc.)
- Specific - Class in org.anchoranalysis.plugin.mpp.bean.region
-
- Specific() - Constructor for class Specific
-
- SpecificAndRename - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects a specific set of channels from stacks, each identified by a stack-name and channel index
- SpecificAndRename() - Constructor for class SpecificAndRename
-
- SpecificAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
A feature based one one-specific principal-axis as identified by image moments.
- SpecificAxisBase() - Constructor for class SpecificAxisBase
-
- SpecificDisabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Only specific outputs, identified by a textual name, are disabled, and all others are enabled.
- SpecificDisabled() - Constructor for class SpecificDisabled
-
- SpecificDisabled(StringSet) - Constructor for class SpecificDisabled
-
- SpecificEnabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Only specific outputs, identified by a textual name, are enabled.
- SpecificEnabled() - Constructor for class SpecificEnabled
-
- SpecificEnabled(StringSet) - Constructor for class SpecificEnabled
-
- SpecificEnergyChannelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
-
- SpecificEnergyChannelBase() - Constructor for class SpecificEnergyChannelBase
-
- SpecificPathList - Class in org.anchoranalysis.io.input.bean.files
-
A specific list of paths which form the input.
- SpecificPathList(List<String>) - Constructor for class SpecificPathList
-
- SpecificPathList(StringList) - Constructor for class SpecificPathList
-
- SpecificPathList() - Constructor for class SpecificPathList
-
- SpecifyDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider
-
Specifies dimensions explicitly via bean properties.
- SpecifyDimensions(int, int) - Constructor for class SpecifyDimensions
-
Create with specific lengths for X and Y dimensions.
- SpecifyDimensions(SizeXY) - Constructor for class SpecifyDimensions
-
Create with specific lengths for X and Y dimensions.
- SpecifyDimensions() - Constructor for class SpecifyDimensions
-
- Sphere - Class in org.anchoranalysis.mpp.mark.conic
-
A sphere
- Sphere(Bound) - Constructor for class Sphere
-
Creates with a radius within particular bounds.
- Sphere(Sphere) - Constructor for class Sphere
-
Copy Constructor
- Sphere() - Constructor for class Sphere
-
- split(Path) - Method in class RootPath
-
It splits the root portion of a path from the remainder.
- split(Path, String, boolean) - Method in class RootPathMap
-
Given a path, it splits the *root* portion of the path from the remainder, trying a root
identified by the rootName and debugMode (and if this fails, also trying with
debugMode==false)
- SplitByObjects - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
-
- SplitByObjects() - Constructor for class SplitByObjects
-
- SplitContourAtSaddlePoints - Class in org.anchoranalysis.plugin.points.bean
-
Splits a 2D contour represented by an object-mask into several contours, splitting at "turn"
points.
- SplitContourAtSaddlePoints() - Constructor for class SplitContourAtSaddlePoints
-
- splitFilename(String) - Static method in class ExtensionUtilities
-
Splits the file-name of a path into a base part and an extension part.
- SplitIntoSquares - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
-
Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
- SplitIntoSquares() - Constructor for class SplitIntoSquares
-
- SplitPath - Class in org.anchoranalysis.core.system.path
-
A path that has been split into two components: a root and a remainder.
- SplitPath(Path, Path) - Constructor for class SplitPath
-
- Stack - Class in org.anchoranalysis.image.core.stack
-
One or more single-channel images that all have the same dimensions.
- Stack() - Constructor for class Stack
-
Creates a new empty
Stack that will not become an RGB image after adding channels.
- Stack(boolean) - Constructor for class Stack
-
Creates a new empty
Stack and whether it will become an RGB image or not.
- Stack(Channel) - Constructor for class Stack
-
Creates a
Stack with a single channel.
- Stack(Extent) - Constructor for class Stack
-
Creates a
Stack with a single
unsigned-byte channel of size
channel.
- Stack(Dimensions, ChannelFactorySingleType, int, boolean) - Constructor for class Stack
-
Create with a particular number of empty
Channels.
- Stack(boolean, Channel...) - Constructor for class Stack
-
Creates from a varying number of channels, and a flag to indicate if they represent an RGB
image or not.
- Stack(Stream<Channel>) - Constructor for class Stack
-
- Stack(boolean, Stream<Channel>) - Constructor for class Stack
-
Like
Stack(Stream) but allows explicitly setting whether it should be interpreted as
RGB or not.
- stack() - Method in class MultiInput
-
- stack(String) - Static method in class ReferenceFactory
-
- StackGenerator - Class in org.anchoranalysis.image.io.stack.output.generator
-
Writes a stack to the filesystem.
- StackGenerator(String, boolean) - Constructor for class StackGenerator
-
Creates a generator that performs no padding.
- StackGenerator(boolean, Optional<String>, boolean) - Constructor for class StackGenerator
-
Creates the generator from a stack, inferring whether all stacks will be 2D from this stack's
dimensions.
- StackGenerator(boolean, Optional<String>, StackWriteAttributes) - Constructor for class StackGenerator
-
- StackIdentifiers - Class in org.anchoranalysis.image.io.stack
-
Common identifiers used for storing particular types of images.
- StackNotUniformSized - Class in org.anchoranalysis.image.core.stack
-
A list of
Channels that are permitted to vary in size.
- StackNotUniformSized() - Constructor for class StackNotUniformSized
-
Creates an empty with no channels.
- StackNotUniformSized(Stream<Channel>) - Constructor for class StackNotUniformSized
-
- StackNotUniformSized(Channel) - Constructor for class StackNotUniformSized
-
- StackProvider - Class in org.anchoranalysis.image.bean.provider.stack
-
- StackProvider() - Constructor for class StackProvider
-
- StackProviderUnary - Class in org.anchoranalysis.image.bean.provider.stack
-
- StackProviderUnary() - Constructor for class StackProviderUnary
-
- StackProviderWithLabel - Class in org.anchoranalysis.image.io.bean.stack.combine
-
- StackProviderWithLabel(Stack, String) - Constructor for class StackProviderWithLabel
-
- StackProviderWithLabel() - Constructor for class StackProviderWithLabel
-
- StackReader - Class in org.anchoranalysis.image.io.bean.stack.reader
-
Reads an image-
Stack from the file-system.
- StackReader() - Constructor for class StackReader
-
- StackReaderOrientationCorrection - Class in org.anchoranalysis.image.io.bean.stack.reader
-
A
StackReader that supports the correction of orientation as images are read from the
file-system.
- StackReaderOrientationCorrection() - Constructor for class StackReaderOrientationCorrection
-
- StackRGBState - Enum in org.anchoranalysis.image.io.stack.output
-
Whether a stack is RGB or RGBA or neither.
- stacks(Logger) - Method in class AnnotationWithStrategy
-
All stacks associated with the input, lazily evaluated.
- stacks() - Method in class ImageInitialization
-
- STACKS - Static variable in class OutputterDirectories
-
Where stacks are typically placed in a define-experiment output
- Stacks - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
- Stacks(InputManager<FileInput>) - Constructor for class Stacks
-
- Stacks() - Constructor for class Stacks
-
- StackSequenceInput - Interface in org.anchoranalysis.image.io.stack.input
-
Provides a single stack (or a time series of such stacks) as an input
- StackSeries - Class in org.anchoranalysis.image.io.stack
-
- StackSeries() - Constructor for class StackSeries
-
- stackTrace() - Method in exception AnchorFriendlyCheckedException
-
Prints a stack trace of the current exception to a string.
- StackWithMap - Class in org.anchoranalysis.mpp.io.input
-
Combines a Stack with a map of other stacks
- StackWithMap(String, ProvidesStackInput) - Constructor for class StackWithMap
-
- StackWriteAttributes - Class in org.anchoranalysis.image.io.stack.output
-
Attributes describing stack which may determine which writer is used.
- StackWriteAttributes(boolean, boolean, boolean, StackRGBState, boolean) - Constructor for class StackWriteAttributes
-
Alternative constructor that assumes each channel is 8-bits.
- StackWriteAttributesFactory - Class in org.anchoranalysis.image.io.stack.output
-
- StackWriteOptions - Class in org.anchoranalysis.image.io.stack.output
-
A combination of attributions describing how to write a particular stack and any suggestions from
the user.
- StackWriteOptions(StackWriteAttributes, Optional<ImageFileFormat>) - Constructor for class StackWriteOptions
-
- StackWriter - Class in org.anchoranalysis.image.io.bean.stack.writer
-
Writes a stack (i.e.
- StackWriter() - Constructor for class StackWriter
-
- StackWriterDelegateBase - Class in org.anchoranalysis.plugin.io.bean.stack.writer
-
- StackWriterDelegateBase() - Constructor for class StackWriterDelegateBase
-
- StandardDeviation - Class in org.anchoranalysis.feature.bean.results
-
The standard-deviation of the results from a particular feature.
- StandardDeviation() - Constructor for class StandardDeviation
-
- standardDeviation() - Method in class Histogram
-
Calculates the standard-deviation of the distribution represented by the histogram.
- start() - Method in class StatefulNullMessageLogger
-
- start() - Method in class ConsoleMessageLogger
-
- start() - Method in class FailureOnlyMessageLogger
-
- start() - Method in class MessageLoggerList
-
- start() - Method in interface StatefulMessageLogger
-
- start() - Method in class TextFileMessageLogger
-
- start(FeatureInitialization, SharedFeatures, Logger) - Method in class SequentialSession
-
Starts the session
- start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in interface FeatureTableCalculator
-
Initializes a feature store that has the same structure as that previously created by
createFeatures() from the same object
- start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class PairsTableCalculator
-
- start(ImageInitialization, Optional<EnergyStack>, Logger) - Method in class SingleTableCalculator
-
- start() - Method in class TextFileOutput
-
- start(EnergyStack) - Method in class CheckMark
-
- start(FeedbackBeginParameters<T>) - Method in class AggregateTriggerBank
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class DiscardOutliers
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class RelationWithMatches
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class GreaterIntersectionWith
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class IntensityGreaterEqualThan
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class IntersectsWith
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ThresholdedFeature
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ThresholdedVolume
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ObjectFilterPredicate
-
- start(Optional<Dimensions>, ObjectCollection) - Method in class ObjectFilterRelation
-
- start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class OutlinePreserveRelativeSize
-
- start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class ThumbnailFromObjects
-
Initializes a batch to create thumbnails.
- start() - Method in class ScaleToSize
-
- start() - Method in class ThumbnailFromStack
-
- start(EnergyStack) - Method in class AndList
-
- start(EnergyStack) - Method in class FeatureValueCheckMark
-
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class CombineObjectsForFeatures
-
Derives a list of inputs from an object-collection
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class EachObjectIndependently
-
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class PairNeighbors
-
- startSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class ConvertImageFormat
-
- startSeries(S, U, InputOutputContext) - Method in class RasterTask
-
Starts processing of a series.
- startSeries(OutputSequenceIncrementing<Stack>, NoSharedState, InputOutputContext) - Method in class MovieFromSlices
-
- StatefulMessageLogger - Interface in org.anchoranalysis.experiment.log
-
A
MessageLogger that can be started and stopped, and is aware this state.
- StatefulNullMessageLogger - Class in org.anchoranalysis.experiment.bean.log
-
Does nothing (i.e.
- StatefulNullMessageLogger() - Constructor for class StatefulNullMessageLogger
-
- StateReporter<T,S> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
-
Converts the optimization state to a form that the reporter needs
- StateReporter() - Constructor for class StateReporter
-
- stateReporter() - Method in class AssignMode
-
- stateReporter() - Method in class DirectAssignMode
-
- stateReporter() - Method in class TransformationAssignMode
-
- StateReporterIdentity<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
Assumes the state is reported without any transformation
- StateReporterIdentity() - Constructor for class StateReporterIdentity
-
- StateReporterToPixelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
Assumes we are interested in
VoxelizedMarksWithEnergy as reporting type, and our
optimization-state is in the form
ToPixelized<T>
- StateReporterToPixelized() - Constructor for class StateReporterToPixelized
-
- StateReporterTransformer<T,S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
- StateReporterTransformer() - Constructor for class StateReporterTransformer
-
- stateToKernel() - Method in class KernelStateBridge
-
- stateToKernel() - Method in class KernelStateBridgeIdentity
-
- stateToKernel() - Method in class KernelStateBridgePixelize
-
- stateToKernel() - Method in class KernelStateBridgeTransformer
-
- StateTransformer<W,X> - Interface in org.anchoranalysis.mpp.segment.transformer
-
- StateTransformerBean<S,T> - Class in org.anchoranalysis.mpp.segment.transformer
-
Transforms one type into another
- StateTransformerBean() - Constructor for class StateTransformerBean
-
- StaticFilePath - Class in org.anchoranalysis.plugin.io.bean.file.path
-
- StaticFilePath() - Constructor for class StaticFilePath
-
- StatisticalBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.statistics
-
Calculates a score based upon the statistical mean and std-deviation.
- StatisticalBase() - Constructor for class StatisticalBase
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class FeatureResultsStatistic
-
Calculates the statistic for a given list of result-value.
- statisticFromFeatureValue(DoubleArrayList) - Method in class Mean
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class Quantile
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class StandardDeviation
-
- statisticFromFeatureValue(DoubleArrayList) - Method in class Sum
-
- statistics() - Method in interface Assignment
-
The statistics associated with the assignment.
- statistics() - Method in class ObjectVoxelIntersection
-
- statistics() - Method in class OverlappingObjects
-
- statisticsFor(int, int, int) - Method in interface VoxelizedMark
-
- statisticsForAllGroups() - Method in class ComparisonSharedState
-
- statisticsForAllSlices(int, int) - Method in interface VoxelizedMark
-
- statisticsForAllSlices(VoxelizedMark, boolean) - Method in class SelectSlicesWithIndexBase
-
- statisticsForAllSlicesMaskSlice(int, int, int) - Method in interface VoxelizedMark
-
- StatisticsToExport - Class in org.anchoranalysis.annotation.io.comparer
-
Statistics to be exported, comprised of name-value pairs.
- StatisticsToExport() - Constructor for class StatisticsToExport
-
- stdDev() - Method in interface VoxelStatistics
-
The standard-deviation of all voxel values.
- StdDev - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- StdDev() - Constructor for class StdDev
-
- Steepest - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
-
- Steepest(SlidingBuffer<?>, WatershedEncoding, boolean, boolean, Optional<ObjectMask>) - Constructor for class Steepest
-
Create for a specific buffer.
- steepestDescent(Point3i, int, int) - Method in class Steepest
-
- StoreSupplier<T> - Interface in org.anchoranalysis.core.identifier.provider.store
-
Supplier of an object for a store.
- stream() - Method in class DoubleSet
-
Creates a stream of elements in the set.
- stream() - Method in class IntegerSet
-
Creates a stream of elements in the set.
- stream() - Method in class StringSet
-
Creates a stream of elements in the set.
- stream() - Method in class StreamableCollection
-
A single instance of the stream from the supplier.
- stream() - Method in class NameValueMap
-
Exposes the elements in the set as a stream.
- stream() - Method in class ResultsVectorList
-
- stream() - Method in class ObjectCollection
-
Provides various functional-programming operations on the object-collection.
- stream() - Method in class ImageCounterList
-
- stream() - Method in class BoundedList
-
A stream of elements in the list.
- StreamableCollection<T> - Class in org.anchoranalysis.core.functional
-
As a stream can only be used once, this data-structure allows for repeatedly getting streams from
a collection.
- StreamableCollection(Collection<T>) - Constructor for class StreamableCollection
-
Create for a particular collection
- StreamableCollection(Supplier<Stream<T>>) - Constructor for class StreamableCollection
-
- streamIndices(Collection<Integer>) - Method in class ObjectCollection
-
Streams only objects at specific indices.
- streamOverZ() - Method in class Extent
-
Streams over the range of z values.
- streamStandardJava() - Method in class ObjectCollection
-
A stream of object-masks as per Java's standard collections interface.
- StringGenerator - Class in org.anchoranalysis.io.generator.text
-
- StringGenerator() - Constructor for class StringGenerator
-
- StringList - Class in org.anchoranalysis.bean.primitive
-
A bean defining a list of
Strings.
- StringList() - Constructor for class StringList
-
Constructs with an empty list.
- StringList(String...) - Constructor for class StringList
-
Constructs, populated with one or more values.
- StringList(List<String>) - Constructor for class StringList
-
Constructs, populated with a list of strings.
- StringListFactory - Class in org.anchoranalysis.bean.xml.factory.primitive
-
- StringListFactory() - Constructor for class StringListFactory
-
- StringMap - Class in org.anchoranalysis.bean.shared
-
A bean that defines a mapping between a set of
Strings to another set of
Strings.
- StringMap() - Constructor for class StringMap
-
- StringMapItem - Class in org.anchoranalysis.bean.shared
-
A bean with a pair of strings, representing a mapping from one string to the other.
- StringMapItem() - Constructor for class StringMapItem
-
- stringRepresentationForElement(int) - Method in interface IncompleteElementRange
-
Returns the typed-index corresponding to the integer-index.
- StringSet - Class in org.anchoranalysis.bean.primitive
-
A bean defining a set of
Strings.
- StringSet(String...) - Constructor for class StringSet
-
Constructs with one or more values added to the list.
- StringSet() - Constructor for class StringSet
-
- StringSet(Set<String>) - Constructor for class StringSet
-
- StringSetFactory - Class in org.anchoranalysis.bean.xml.factory.primitive
-
- StringSetFactory() - Constructor for class StringSetFactory
-
- StringSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
- StringSuffixOutputNameStyle() - Constructor for class StringSuffixOutputNameStyle
-
- StringSuffixOutputNameStyle(String, Optional<String>) - Constructor for class StringSuffixOutputNameStyle
-
- StringsWithoutOrder - Class in org.anchoranalysis.io.manifest.sequencetype
-
A sequence of strings that has no order.
- StringsWithoutOrder() - Constructor for class StringsWithoutOrder
-
- StringUtilities - Class in org.anchoranalysis.core.value
-
Utility functions for manipualting strings.
- strMarks() - Method in class MarkWithPositionAndSingleRadius
-
- strPos() - Method in class MarkWithPosition
-
- subdirectories() - Method in class MutableDirectory
-
- Subdirectory - Class in org.anchoranalysis.io.manifest.directory
-
- Subdirectory(Path) - Constructor for class Subdirectory
-
- Subdirectory() - Constructor for class Subdirectory
-
- subdirectory(String, ManifestDirectoryDescription, boolean) - Method in interface InputOutputContext
-
Creates a new context that writes instead to a subdirectory.
- SubdirectoryBase - Class in org.anchoranalysis.io.manifest.directory
-
- SubdirectoryBase(Path) - Constructor for class SubdirectoryBase
-
- SubdirectoryBase() - Constructor for class SubdirectoryBase
-
- subdirectoryForGroupOutputs() - Method in class GroupedStackBase
-
An optional subdirectory where the group outputs are placed.
- subdirectoryForGroupOutputs() - Method in class ExportImageHistograms
-
- subdirectoryForGroupOutputs() - Method in class GroupedMeanChannelTask
-
- subList(int, int) - Method in class UpdatableMarksList
-
- SUBMARK_CORE - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_CORE_INNER - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_INSIDE - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_OUTSIDE - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_SHELL - Static variable in class GlobalRegionIdentifiers
-
- SUBMARK_SHELL_OUTSIDE - Static variable in class GlobalRegionIdentifiers
-
- SubmittedJob - Class in org.anchoranalysis.experiment.task.processor
-
- SubmittedJob(JobDescription, JobState) - Constructor for class SubmittedJob
-
- subset(StringSet) - Method in class NamedStacks
-
Creates a new collection containing only items whose keys exist in a particular set.
- subsetCompatibleWith(Class<? extends FeatureInput>) - Method in class SharedFeatures
-
Extracts the subset of inputs that are compatible with a particular input-type.
- SubsetRangeIfRequested - Class in org.anchoranalysis.plugin.io.bean.file.namer
-
If specified in the context, the existing name if subsetted according to an index range.
- SubsetRangeIfRequested() - Constructor for class SubsetRangeIfRequested
-
- subsetWhereBBoxIntersects(Dimensions, int, List<BoundingBox>) - Method in class ColoredMarks
-
- subsetWhereBBoxIntersects(Dimensions, DrawOverlay, List<BoundingBox>) - Method in class ColoredOverlayCollection
-
- SubstituteRegularExpression - Class in org.anchoranalysis.plugin.io.bean.file.copy.naming
-
A regular expression substitution (replaceAll) is applied to the relative-path
- SubstituteRegularExpression() - Constructor for class SubstituteRegularExpression
-
- subtract(VarianceCalculatorDouble) - Method in class VarianceCalculatorDouble
-
- subtract(VarianceCalculatorLong) - Method in class VarianceCalculatorLong
-
- subtract(Tuple3d) - Method in class Tuple3d
-
Arithmetically subtract a
Tuple3d's values across each dimension.
- subtract(int) - Method in class Tuple3i
-
Arithmetically subtracts a value across each dimension.
- subtract(ReadableTuple3i) - Method in class Tuple3i
-
Arithmetically subtracts a value across each dimension.
- subtractFrom(int) - Method in interface VoxelsArithmetic
-
Subtracts all current voxel-values from a constant-value.
- SubtractFrom<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
- SubtractFrom() - Constructor for class SubtractFrom
-
- SubtractFromConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- SubtractFromConstant() - Constructor for class SubtractFromConstant
-
- subtractFromMaxValue() - Method in class VoxelsUntyped
-
Subtracts all voxel-values from the maximum value associated with the data-type.
- SubtractMean - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Subtract the mean (of the entire channel or a masked portion thereof) from every voxel
- SubtractMean() - Constructor for class SubtractMean
-
- SubtractReducedFromMerged - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
- SubtractReducedFromMerged() - Constructor for class SubtractReducedFromMerged
-
- SubtractSecondFromFirst - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Subtract second-object from first-object in a pair.
- SubtractSecondFromFirst() - Constructor for class SubtractSecondFromFirst
-
- SubtractTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
- SubtractTwoChannels(IntBinaryOperation) - Constructor for class SubtractTwoChannels
-
- suffixStringForMeters(SpatialUnits.UnitSuffix) - Static method in class SpatialUnits
-
A string that describes the suffix for meters.
- SuggestionFormatException - Exception in org.anchoranalysis.image.core.dimensions.size.suggestion
-
- SuggestionFormatException(String) - Constructor for exception SuggestionFormatException
-
Create with a message only.
- Sum<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
-
Sums the results after calculating a list of
Features.
- Sum(FeatureList<T>) - Constructor for class Sum
-
Create with a list of
Features which become summed.
- Sum() - Constructor for class Sum
-
- Sum - Class in org.anchoranalysis.feature.bean.results
-
The sum of the results from a particular feature.
- Sum() - Constructor for class Sum
-
- sum() - Method in interface VoxelStatistics
-
The sum of all voxel values.
- sum() - Method in class VoxelStatisticsCombined
-
- sum() - Method in class VoxelStatisticsFromHistogram
-
- sum() - Method in class AggIDCounter
-
- Sum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
- Sum() - Constructor for class Sum
-
- sumExecutionTimeSeconds() - Method in class RecordedExecutionTimes.RecordedOperation
-
The total summed execution time in seconds for the operation.
- summarize() - Method in exception BeanMisconfiguredXMLException
-
This summarize() option just looks for the most deep exception that can be 'combined' and
takes its message
- summarize() - Method in exception LocalisedBeanException
-
- summarize() - Method in exception AnchorCombinableException
-
Creates a new {link Throwable} that summarizes this exception and any nested causes of the
exception.
- summarize() - Method in exception NamedProviderGetException
-
- SummarizeBase<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.task
-
- SummarizeBase() - Constructor for class SummarizeBase
-
- summarizeDisabled() - Method in class RecordedOutputs
-
A comma-separated string of all output-names that were not enabled.
- summarizeEnabled() - Method in class RecordedOutputs
-
A comma-separated string of all output-names that were enabled.
- summarizeIgnoreIdenticalFilePath(Path) - Method in exception LocalisedBeanException
-
If there is no nested-set of combinable exceptions, and the
message related to this
current exception is identical as the passed parameter, then we simply ignore the current
exception and promote its
Throwable.getCause().
- SummarizeInputs<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.task
-
- SummarizeInputs() - Constructor for class SummarizeInputs
-
- summarizeMultiplex(boolean) - Method in class RecordedOutputs
-
- Summarizer<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Summarizes a set of elements by outputting a descriptive string.
- Summarizer() - Constructor for class Summarizer
-
- SummarizerAggregate<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Collects summary data about a set of input files that will eventually be outputted to the user
- SummarizerAggregate() - Constructor for class SummarizerAggregate
-
- SummarizerCount<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
A count of the number of inputs.
- SummarizerCount() - Constructor for class SummarizerCount
-
- SummarizerImageMetadata<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
- SummarizerImageMetadata() - Constructor for class SummarizerImageMetadata
-
- SummarizerImageMetadataSimple<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
A simple summarizer, where there's one summary-item per image.
- SummarizerImageMetadataSimple() - Constructor for class SummarizerImageMetadataSimple
-
- SummarizerInputFromManager<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
-
Extracts a particular item from an
InputFromManager for further summarization downstream.
- SummarizerInputFromManager() - Constructor for class SummarizerInputFromManager
-
- SummarizerListMultiline<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Creates a string where each line is an element.
- SummarizerListMultiline() - Constructor for class SummarizerListMultiline
-
- SummarizerPath - Class in org.anchoranalysis.plugin.io.bean.summarizer.path
-
Base class for
Summarizers that operate on the
Path associated with inputs.
- SummarizerPath() - Constructor for class SummarizerPath
-
- SummarizerSplitMoreThan<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Multiplexes between two summarizers depending on the total number of count.
- SummarizerSplitMoreThan() - Constructor for class SummarizerSplitMoreThan
-
- SummaryException - Exception in org.anchoranalysis.core.exception.combinable
-
A special kind of exception that represents a summary of an existing set of exceptions.
- SummaryException(String, Throwable) - Constructor for exception SummaryException
-
Creates with a message and a cause.
- sumOfSquares() - Method in interface VoxelStatistics
-
The sum of the square of all voxel values.
- sumOfSquares() - Method in class VoxelStatisticsCombined
-
- sumOfSquares() - Method in class VoxelStatisticsFromHistogram
-
- sumOverlapFromPaired() - Method in class OverlappingObjects
-
Sums the overlap-ratio across all assigned pairs.
- SupplierAtIndex<T> - Interface in org.anchoranalysis.io.manifest.directory.sequenced
-
- supportsMultipleChannelsPerSourceBuffer() - Method in class ConvertTo
-
Whether the source buffer can encode more than one channel?
- supportsMultipleChannelsPerSourceBuffer() - Method in class ToUnsignedByteWithScaling
-
- supportsMultipleChannelsPerSourceBuffer() - Method in class UnsignedByteFromFloat
-
- supportsMultipleChannelsPerSourceBuffer() - Method in class UnsignedByteFromUnsignedByte
-
- supportsMultipleChannelsPerSourceBuffer() - Method in class ToFloat
-
- supportsMultipleChannelsPerSourceBuffer() - Method in class UnsignedIntFromUnsignedInt
-
- supportsMultipleChannelsPerSourceBuffer() - Method in class ToUnsignedShort
-
- SupportsTimeSeries - Class in org.anchoranalysis.io.imagej.bean.stack.writer
-
- SupportsTimeSeries() - Constructor for class SupportsTimeSeries
-
- suppressedLogger() - Static method in class LoggingFixture
-
A
Logger that doesn't output anything.
- suppressedMessageLogger() - Static method in class LoggingFixture
-
- SurfaceNumberVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
The number of voxel-faces along the surface (the faces of each voxel that touch outside)
- SurfaceNumberVoxelFaces() - Constructor for class SurfaceNumberVoxelFaces
-
- SurfaceNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
The number of voxels on the surface (all voxels on the exterior of the object)
- SurfaceNumberVoxels() - Constructor for class SurfaceNumberVoxels
-
- SurfaceNumberVoxelsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
- SurfaceNumberVoxelsBase() - Constructor for class SurfaceNumberVoxelsBase
-
- SurfaceSizeMaskNonZero - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
-
- SurfaceSizeMaskNonZero() - Constructor for class SurfaceSizeMaskNonZero
-
- SwitchChannelTime - Class in org.anchoranalysis.io.bioformats.bean.options
-
Treats the channel index as if it's time, and vice versa
- SwitchChannelTime() - Constructor for class SwitchChannelTime
-
- SwitchDetailedLogging - Class in org.anchoranalysis.experiment.bean.log
-
Switches between two log-reporters depending on whether detailed logging is switched on or not
- SwitchDetailedLogging() - Constructor for class SwitchDetailedLogging
-